vg chunk on a minigraph-CACTUS graph returns an error because vg can no longer accept a GFA with P lines and rGFA lines that describe the same path

[Overcraft90]

1. What were you trying to do? My aim is to split the graph in chromosomes (ideally) so that I can visualize them in Bandage

2. What did you want to happen? I was expecting the following command

vg chunk -x /g100_scratch/userexternal/mungaro0/pangenomes/2.human-pgV2/human-pgV2.gfa -t 48 > /g100_scratch/userexternal/mungaro0/human-pgV2_chunk.vg

to use vg chunk to divide the graph into major chromosomes to be visualized in a 2D view. 3. What actually happened? The tool returned an error related to possible file corruption. However, I checked both the integrity and consistency of the original .gz output from minigraph-CACTUS as well as the .gfa file I fed to vg. They both seem fine but this is the output for the error I get

error[register_loader_saver_gfa] GFA file /g100_scratch/userexternal/mungaro0/pangenomes/2.human-pgV2/human-pgV2.gfa is corrupt and cannot be loaded.
GFA format error: On pass 1: On line 53471402: Duplicate path GRCh38.chr1 would be created in graph

4. If you got a line like Stack trace path: /somewhere/on/your/computer/stacktrace.txt, please copy-paste the contents of that file here:

Place stacktrace here.

5. What data and command can the vg dev team use to make the problem happen? A minigraph-CACTUS graph built upon GRCh38 for five human individuals on which to run the vg chunk command.

6. What does running vg version say?

vg version v1.42.0 "Obolo"
Compiled with g++ (Ubuntu 11.2.0-19ubuntu1) 11.2.0 on Linux
Linked against libstd++ 20220324
Built by ubuntu@ip-172-31-12-246

P.S. I'm not sure about the second line for the error..., it seems something is wrong with the name of the FASTA headers in the reference (which I changed to be more comprehensible); nonetheless, there are no headers with the same name. Hence, I'm not sure about the "Duplicate path" statement

[glennhickey]

Hmm. One quick thing to try as a work-around would be to use the vg included in cactus which I believe is 1.4.0.

[Overcraft90]

@glennhickey Thanks a lot, still getting an error but this time I can at least figure out what is referring to, following the .log output

warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270517.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270515.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270466.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270744.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270709.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270467.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270931.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270929.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270732.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270923.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270917.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270915.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270914.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270891.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270888.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270884.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270883.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-KI270758.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL949752.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-GL000256.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-GL000254.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KI270935.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL949749.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-GL000253.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL949748.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270442.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270926.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-GL000252.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-KI270925.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KI270924.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL949747.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270908.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-JH159148.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KI270904.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270902.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270927.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270900.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270901.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_unloc-KI270729.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KI270899.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-GL000251.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-KI270897.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KI270895.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-KI270881.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KI270877.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KI270878.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-GL383581.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270918.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-GL383580.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-GL383579.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-KI270874.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr20_gen_cont-GL383578.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr20_gen_cont-KI270871.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270590.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr20_gen_cont-GL383577.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270867.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL383575.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KI270863.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-GL383569.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-GL383571.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-GL383570.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-GL383567.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270859.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-GL383564.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270857.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270861.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-GL383556.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KI270853.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KI270855.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270330.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KI270856.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KI270850.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_con-GL000209.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-GL383555.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KI270848.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KI270851.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_gen_cont-KI270845.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_gen_cont-KI270844.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KI270841.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270933.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KI270843.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KI270839.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KI270836.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KI270833.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-GL383551.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-GL383553.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KI270835.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-GL383549.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-GL877876.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-GL877875.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270826.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270829.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270831.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270832.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-GL383545.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270889.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-GL383541.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-GL383540.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270815.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270816.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270819.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270810.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270814.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270822.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270813.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270811.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KI270934.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270812.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270818.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KI270807.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KI270808.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-GL383534.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KI270806.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-KI270798.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-ML143371.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KI270801.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KI270875.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-GL383533.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-GL383552.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KI270837.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_con-KI270795.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270518.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_con-KI270796.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_con-KI270794.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-GL949742.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270882.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-GL383557.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_con-KI270793.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_con-GL000258.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_con-KI270786.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_con-KI270789.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_con-KI270785.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-KI270799.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-GL383527.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_con-KI270788.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_con-KI270790.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KI270849.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_con-KI270784.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_con-KI270782.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_con-KI270779.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_con-KI270781.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_con-KI270778.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_con-KI270777.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_con-KI270780.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_con-KI270783.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270750.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-JH636055.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270767.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270776.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-GL582966.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270768.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270771.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270775.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270772.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-GL383521.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270774.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270773.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270770.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KI270892.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_con-KI270761.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_con-KI270759.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-GL383546.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_con-KI270763.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-GL383518.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr20_gen_cont-KI270869.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_con-KI270765.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_con-KI270760.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_con-KI270766.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-GL383554.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_con-KI270769.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrY_gen_cont-KN196487.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrY_gen_cont-KZ208924.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrY_gen_cont-MU273398.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KI270854.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-ML143384.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-MU273396.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-ML143381.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-MU273394.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-MU273393.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-ML143382.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KI270809.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-ML143385.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-KV766199.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KQ759762.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273344.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270379.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KN538360.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-MU273330.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-MU273359.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KN196473.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KN538361.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL949753.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KB021644.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KV766192.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KZ208917.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-GL383547.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000218.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KZ559100.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000214.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270329.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270757.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270529.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270376.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270507.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270916.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-MU273336.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270755.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-KI270880.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270748.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270747.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270749.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000226.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-ML143357.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270583.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000195.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-GL383519.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL949746.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270521.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270736.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270373.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL949750.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-GL383582.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270372.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-ML143350.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000213.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270385.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_unloc-KI270728.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270866.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KQ983255.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KN196476.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270381.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-MU273363.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_con-KI270762.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270391.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-MU273335.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270587.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270591.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270706.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KI270868.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270383.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270374.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270378.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270448.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KZ559103.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270920.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KZ559109.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270363.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-KQ983258.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270336.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-KV575243.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KI270879.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270338.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KQ031383.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270817.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrY_gen_cont-KZ208923.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270334.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270588.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KV880766.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270862.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270589.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270418.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270579.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-GL383532.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270754.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270580.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-GL000255.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270548.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270712.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270544.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KI270803.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_unloc-GL000205.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_unloc-KI270726.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KN196484.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270386.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-ML143342.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270903.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270738.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270731.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270737.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270921.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270890.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270733.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-MU273391.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270743.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KI270804.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270425.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_gen_cont-KZ208919.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270581.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KI270906.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KZ559113.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575252.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000216.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270465.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_unloc-KI270721.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575251.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-ML143383.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270746.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-KI270894.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575247.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_unloc-GL000009.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-GL383530.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270429.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KI270876.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KZ208921.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270858.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270364.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270741.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_unloc-KI270719.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_unloc-KI270727.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270530.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-ML143347.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270509.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KQ458383.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_con-GL000257.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270422.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270593.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270713.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-ML143354.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270412.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KI270936.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr20_gen_cont-MU273388.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KZ208906.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270371.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270396.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-JH159137.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270742.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270311.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270734.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270512.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270714.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KZ208904.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-MU273361.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-JH159147.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KN196474.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270753.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270388.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KQ458382.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270584.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KZ208912.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_unloc-KI270715.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KZ208905.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270335.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KV766197.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000224.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270392.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-KI270824.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270735.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_unloc-KI270718.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KQ458384.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-MU273364.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-MU273334.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270362.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_unloc-GL000194.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-KI270913.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_unloc-GL000008.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_unloc-KI270720.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-KI270896.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_con-KI270791.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_unloc-KI270724.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KZ559102.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-ML143366.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270922.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_unloc-GL000221.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270711.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-KI270823.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270820.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270387.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-KV766193.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL383576.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-MU273397.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270312.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270333.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575249.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270302.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575257.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270887.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-MU273355.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270310.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270752.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr20 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270322.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_unloc-GL000208.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_unloc-KI270716.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-ML143360.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270419.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_con-KI270764.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KV880764.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_unloc-KI270725.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270390.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270320.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-GL383522.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-ML143356.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270315.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270375.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270394.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575259.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KQ090026.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270930.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-ML143345.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_unloc-KI270730.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270389.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270886.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270707.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270305.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270910.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KQ031387.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270303.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-GL383542.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270528.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270435.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-GL383550.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270420.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KQ031386.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270508.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KI270821.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-KZ208907.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-GL339449.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrY as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrY_unloc-KI270740.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270516.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KN196472.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575255.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270304.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270827.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-KQ090018.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270393.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL949751.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270510.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270317.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-MU273333.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270411.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270384.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_unloc-KI270739.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-ML143353.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KI270937.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270414.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-KI270873.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-MU273346.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270424.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_unloc-KI270717.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270756.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-MU273366.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270417.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KI270800.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270382.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-JH159146.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-GL383531.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-MU273353.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270423.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr20_gen_cont-KI270870.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270395.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270468.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-MU273386.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-KV880763.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273343.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KI270852.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KZ208922.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270710.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273340.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KI270834.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273338.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-ML143352.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-GL000250.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KZ559110.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-MU273331.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270538.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-KQ031384.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273342.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-GL383526.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-MU273349.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KZ208914.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270860.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KN196486.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273339.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273341.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_con-KI270787.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-MU273387.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-GL383539.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-KZ208908.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270582.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-KN538363.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-GL383566.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KQ090024.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-ML143341.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-KN538362.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-MU273347.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270919.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KZ559114.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KZ208915.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KV880767.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_gen_cont-KI270847.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KN196475.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-GL383583.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KQ031385.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-ML143377.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KN538364.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KI270911.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-GL383528.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-ML143378.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-ML143343.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KZ208909.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270885.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KZ559104.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-KQ983257.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KZ559105.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-MU273381.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273345.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-ML143344.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-KQ090013.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-ML143348.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-KI270872.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-MU273379.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-ML143346.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KI270830.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-KQ983256.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-KQ090020.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KN538370.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270751.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-KN538366.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-ML143349.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270511.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-KQ090014.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-ML143369.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-GL383563.3 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-KQ090015.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-GL383520.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-KZ208910.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-KN196479.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-MU273356.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-GL383568.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KQ090017.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-KV575244.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-MU273357.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KQ090016.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-ML143351.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KZ559106.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000219.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KZ208913.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_unloc-KI270723.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KQ458385.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-MU273358.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KV880765.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_unloc-GL000225.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_gen_cont-MU273373.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270522.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KQ031388.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-KZ559107.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-MU273360.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-KQ090019.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8_gen_cont-MU273362.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-MU273374.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr9_gen_cont-MU273365.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-ML143355.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KQ759760.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-KN196480.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KI270838.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-KZ559101.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KN538369.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-KQ090021.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-MU273367.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270316.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-MU273351.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-MU273369.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270932.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr8 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-MU273371.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-KN196477.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KN538368.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575258.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KZ559108.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270907.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KV766195.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KI270865.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-GL383565.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-MU273370.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KI270846.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KZ559111.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-ML143359.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KQ090022.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-GL000220.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-MU273368.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KN196481.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KQ090023.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KI270912.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575253.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KI270840.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr4_gen_cont-MU273350.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KZ208916.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KI270905.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_gen_cont-MU273332.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-ML143362.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KN196482.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KZ208918.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-ML143361.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-ML143376.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL383574.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270340.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-ML143363.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chrX_gen_cont-MU273395.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KN196483.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KN538373.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-KI270898.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KI270842.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KQ090025.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-MU273352.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-ML143364.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-ML143365.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_con-KI270797.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KN538371.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_gen_cont-ML143367.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-MU273382.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575256.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr1_unloc-KI270708.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_gen_cont-KZ208920.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270337.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575246.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_gen_cont-ML143368.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KN538374.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-ML143372.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-KQ031389.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr20_gen_cont-MU273389.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-KZ559112.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr14_unloc-KI270722.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-MU273375.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-KI270893.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_con-KI270792.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr12_gen_cont-MU273372.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr15_gen_cont-ML143370.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-GL383573.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-MU273376.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr7_gen_cont-KI270805.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KV880768.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-ML143373.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270366.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KQ090027.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270438.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KQ458386.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KV766194.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-KQ031390.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-GL383572.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr5_gen_cont-MU273354.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr16_gen_cont-MU273377.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KV766196.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-KN538367.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KQ458387.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KI270928.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-ML143374.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-JH159136.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KV575245.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-MU273380.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KI270909.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KN196478.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-MU273378.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-KQ759759.2 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-MU273383.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-ML143375.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KZ559116.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KZ559115.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr13_gen_cont-KN538372.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KQ090028.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr3_gen_cont-MU273348.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-MU273384.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270519.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KZ208911.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-MU273385.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr6_gen_cont-KI270802.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575248.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575250.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575254.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-MU273390.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KB663609.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr2_gen_cont-MU273337.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_gen_cont-KN538365.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr21_gen_cont-MU273392.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr18_gen_cont-KI270864.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KV575260.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-ML143380.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr19_gen_cont-KI270938.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270745.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr17_gen_cont-KV766198.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr11_gen_cont-ML143358.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KN196485.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KQ458388.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr10_unv_ori-KI270825.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-KQ759761.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.unpl_cont-KI270539.1 as a path with that name has already been imported from a P-line
warning:[gfa_to_handle_graph] Ignoring rGFA tags for path GRCh38.chr22_gen_cont-ML143379.1 as a path with that name has already been imported from a P-line
error:[vg chunk] context expansion steps must be specified with -c/--context when chunking on paths

Now, in my command I haven't specified the -c flag, as I didn't know it was necessary. Seems like I need to indicate the number of node steps I would like to extend the chunking operation..., is there a predefined number; otherwise, how can I indicate the whole node/state space for the graph?

Thanks in advance!

[glennhickey]

If you're chunking by chromosome, you can use -C instead of -c (sorry the error message doesn't mention this)

component chunking:
    -C, --components         create a chunk for each connected component.  if a targets given with (-p, -P, -r, -R), limit to components containing them
    -M, --path-components    create a chunk for each path in the graph's connected component

A couple other things:

• If you've made your graph with minigraph-cactus you get chromosome graphs in the cactus-graphmap-join output
• Whole chromosome graphs can still be too big for Bandage. Newer Bandage may help a bit https://github.com/asl/BandageNG/releases/tag/v2022.06 th
• @adamnovak It looks like the released HPRC graphs (which contain redundant P line / rGFA tags for reference path) are incompatible with the current vg release? I think this needs to be downgraded back to a warning as we can't really change the graphs.

[adamnovak]

I changed it to an error because it seemed like a thing nobody would do. If it turns out we do it all the time, we will indeed have to handle it.

[adamnovak]

I have a PR in #3729 that includes a test for reading a GFA like this and downgrades the error to a warning.

The GBWTGraph GFA reader doesn't read the rGFA tags yet, so I don't think it needs to be touched.

[Overcraft90]

Hi @glennhickey,

Thanks a lot again! With the -C flag it works, still the log (vg_chunk.log) file returns some ignored paths; is there any specific reason for that?

Also, the output is a bunch of *chunk_.vg files and I was wondering whether there was a way to get them in .gfa format for Bandage to visualize them correctly. Sorry, in the end I stick with the "old" Bandage, as I didn't really understood how to install the "new" one. Hopefully, this is not an issue e.g the new version allows for visualizing even .vg** files...

Finally, the output for the vg chunk command

vg chunk -x /g100_scratch/userexternal/mungaro0/pangenomes/2.human-pgV2/human-pgV2.gfa -C -t 48 > /g100_scratch/userexternal/mungaro0/human-pgV2_chunk.vg

ia an empty human-pgV2_chunk.vg file, what is that supposed to do/mean? Thanks in advance!

[glennhickey]

The warnings in your log are expected and can be ignored -- more information in #3729.

You can go from vg to gfa with vg convert -f graph.vg > graph.gfa. vg chunk can output gfa with -O gfa.

When outputting multiple files, vg chunk writes nothing to stdout. The output files will be in your working directory prefixed with chunk. You can change this with vg chunk -b.

[Overcraft90]

@glennhickey,

Sorry looking at the vg options I must have overlooked at the flag -O. vg chunk worked just fine, I now have all .gfa files (they are 4539) on a graph built for five human individuals with GRCh38 as backbone.

This time, as per the pggb assembly, I renamed the chunks with a chr string in front to make things a bit clearer; the real problem is that, despite having the chromosomes in the reference with their correct names — I actually renamed all of them to a more humanly comprehensible format — the chunks "i" components are not renamed accordingly.

In other words, I do not have any correspondence between a chromosome in the reference and an actual chunk form vg, same applies to pggb. I don't even know whether this can even be called a problem, as I guess when the pangenome graph is chopped the coordinate system switches from the reference to the real paths structure within the VGS (correct me if I'm wrong). With that said, I think this issue is resolved and we can close it.

Thanks again!