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Arkadiy-Garber / MagicLamp

A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets.
GNU General Public License v3.0
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Error finding *.depth file #5

Open Mariaroviscomonteiro opened 2 years ago

Mariaroviscomonteiro commented 2 years ago

Hello,

I am trying to use LithoGenie to functionally annotate my MAGs. The programme is working fine until I use the -bams option to normalise taking into account the coverage from read mapping (My MAGs were generated from a co-assembly and I made a bam.txt following your instructions for co-assembled genomes).

I keep getting this error:

processing... maxbin.031_sub.contigs.fa Output depth matrix to maxbin.031_sub.contigs.fa.depth jgi_summarize_bam_contig_depths 2.15 (Bioconda) 2020-07-03T13:02:15 Output matrix to maxbin.031_sub.contigs.fa.depth 0: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT31.bam 12: Opening bam: 11: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT52.bam56: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT42.bam /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT53.bam

8: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT44.bam : Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT41.bam 13: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT54.bam 7: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT43.bam 3: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT34.bam 2: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT33.bam 14: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT55.bam 1: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT32.bam 4: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT35.bam 109: Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT51.bam : Opening bam: /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/bin_coverage/BT45.bam Processing bam files Thread 0 finished: BT31.bam with 41784108 reads and 2548900 readsWellMapped Thread 13 finished: BT54.bam with 37818784 reads and 1818920 readsWellMapped Thread 8 finished: BT44.bam with 47649368 reads and 8359982 readsWellMapped Thread 12 finished: BT53.bam with 42732468 reads and 3793898 readsWellMapped Thread 6 finished: BT42.bam with 41398298 reads and 4262408 readsWellMapped Thread 14 finished: BT55.bam with 14976816 reads and 801879 readsWellMapped Thread 7 finished: BT43.bam with 76231146 reads and 12109136 readsWellMapped Thread 10 finished: BT51.bam with 20372246 reads and 805082 readsWellMapped Thread 5 finished: BT41.bam with 52802668 reads and 3544574 readsWellMapped Thread 11 finished: BT52.bam with 28965720 reads and 1986958 readsWellMapped Thread 4 finished: BT35.bam with 34227688 reads and 5284176 readsWellMapped Thread 2 finished: BT33.bam with 21982532 reads and 1772437 readsWellMapped Thread 3 finished: BT34.bam with 33913086 reads and 3600508 readsWellMapped Thread 1 finished: BT32.bam with 61539122 reads and 4501818 readsWellMapped Thread 9 finished: BT45.bam with 77754398 reads and 11829835 readsWellMapped Creating depth matrix file: maxbin.031_sub.contigs.fa.depth Closing most bam files Closing last bam file Finished processing... maxbin.031_sub.contigs.fa Traceback (most recent call last): File "/scale_wlg_nobackup/filesets/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/1.Prodig_anno_renamed/MagicLamp/genies/LithoGenie.py", line 2253, in main depth = open("%s/contigDepths/%s.depth" % (args.out, cell)) FileNotFoundError: [Errno 2] No such file or directory: 'lithogenie_output_bam/contigDepths/maxbin.031_sub.contigs.fa.depth'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/1.Prodig_anno_renamed/MagicLamp/MagicLamp.py", line 30, in LithoGenie.main() File "/scale_wlg_nobackup/filesets/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/1.Prodig_anno_renamed/MagicLamp/genies/LithoGenie.py", line 2265, in main depth = open("%s/contigDepths/%s.depth" % (args.out, cell)) FileNotFoundError: [Errno 2] No such file or directory: 'lithogenie_output_bam/contigDepths/maxbin.031_sub.contigs.fa.depth'

I have noticed that I generated the file "maxbin.031_sub.contigs.fa.depth", however it is not inside the output_directory.

This is the script I used:

MagicLamp.py LithoGenie -bin_dir /nesi/nobackup/nesi00465/raw_data/Chapter_2_version_Sep2/Chapter_2/MAGs/4.Qual_bins/1.Prodig_anno_renamed/MagicLamp/lithogenie_output/ORF_calls -bin_ext faa -out lithogenie_output_bam -bams bams3.txt --orfs

Cheers,

Maria