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dereneaton / ipyrad

Interactive assembly and analysis of RAD-seq data sets
http://ipyrad.readthedocs.io
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No PE fastq pairs detected based on filenames, assuming SE data #557

Closed angelicagallegonar closed 2 months ago

angelicagallegonar commented 5 months ago

I am trying to run ipyrad on a set of fastqs that I previously demultiplexed. I am receiving this error for all the samples: "No PE fastq pairs detected based on filenames, assuming SE data."

I add an example:

fastq file name (HIB_ES_Carnota_17VV19_1R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 R2, or any of these followed by a ' ' or '.'.

File names are as follows, the problem persist if I remove the hyphens after R1 and R2: HIB_ES_Carnota_17VV19_1R1.fastq.gz HIB_ES_Carnota_17VV19_1R2.fastq.gz

angelicagallegonar commented 5 months ago

I have 540 samples, Maybe it has something to do with the volume of samples?

isaacovercast commented 5 months ago

I'm sure it's not a problem with the number of samples.

Can you show me the ipyrad version you're using: ipyrad -v

Can you show me your params file?

Can you show me ls -l | head -n 20 inside the directory with the R1/R2 files?

Cilia77 commented 2 months ago

I am also having the same issue I am using ipyrad 0.9.96

Params file:

------- ipyrad params file (v.0.9.96)------------------------------------------- Hexaplex ## [0] [assembly_name]: Assembly name. Used to name output directories for assembly steps ./ ## [1] [project_dir]: Project dir (made in curdir if not present)

[2] [raw_fastq_path]: Location of raw non-demultiplexed fastq files

                           ## [3] [barcodes_path]: Location of barcodes file

./*.gz ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files denovo ## [5] [assembly_method]: Assembly method (denovo, reference)

[6] [reference_sequence]: Location of reference sequence file

pairddrad ## [7] [datatype]: Datatype (see docs): rad, gbs, ddrad, etc. TGCAGG,CGG ## [8] [restriction_overhang]: Restriction overhang (cut1,) or (cut1, cut2) 5 ## [9] [max_low_qual_bases]: Max low quality base calls (Q<20) in a read 33 ## [10] [phred_Qscore_offset]: phred Q score offset (33 is default and very standard) 6 ## [11] [mindepth_statistical]: Min depth for statistical base calling 6 ## [12] [mindepth_majrule]: Min depth for majority-rule base calling 10000 ## [13] [maxdepth]: Max cluster depth within samples 0.90 ## [14] [clust_threshold]: Clustering threshold for de novo assembly 0 ## [15] [max_barcode_mismatch]: Max number of allowable mismatches in barcodes 2 ## [16] [filter_adapters]: Filter for adapters/primers (1 or 2=stricter) 35 ## [17] [filter_min_trim_len]: Min length of reads after adapter trim 2 ## [18] [max_alleles_consens]: Max alleles per site in consensus sequences 0.05 ## [19] [max_Ns_consens]: Max N's (uncalled bases) in consensus 0.05 ## [20] [max_Hs_consens]: Max Hs (heterozygotes) in consensus 4 ## [21] [min_samples_locus]: Min # samples per locus for output 0.2 ## [22] [max_SNPs_locus]: Max # SNPs per locus 8 ## [23] [max_Indels_locus]: Max # of indels per locus 0.5 ## [24] [max_shared_Hs_locus]: Max # heterozygous sites per locus 1, 0, 0, 0 ## [25] [trim_reads]: Trim raw read edges (R1>, <R1, R2>, <R2) (see docs) 0, 0, 0, 0 ## [26] [trim_loci]: Trim locus edges (see docs) (R1>, <R1, R2>, <R2)

ls -l | head -n 20 results in this: -rw-r--r-- 1 cilia nhmc 104767222 Ιούν 28 23:47 Ht_100R1.fastq.gz -rw-r--r-- 1 cilia nhmc 111808494 Ιούν 28 23:48 Ht_100R2.fastq.gz -rw-r--r-- 1 cilia nhmc 351054229 Ιούν 28 14:19 Ht_10R1.fastq.gz -rw-r--r-- 1 cilia nhmc 372804038 Ιούν 28 14:20 Ht_10R2.fastq.gz -rw-r--r-- 1 cilia nhmc 73944870 Ιούν 28 23:40 Ht_27R1.fastq.gz -rw-r--r-- 1 cilia nhmc 78718934 Ιούν 28 23:40 Ht_27R2.fastq.gz -rw-r--r-- 1 cilia nhmc 69323747 Ιούν 28 21:39 Ht_31R1.fastq.gz

Demultiplexing (step1) was also conducted in ipyrad to get those fastq.gz files.

Thank you, Cilia

isaacovercast commented 2 months ago

Hi Cilia, Can you show me the full path to the fastqs directory and ls -l on that directory as well? Can you post the full error message from when you run step 1? I'm having a hard time reproducing this error.

isaacovercast commented 2 months ago

I suspect that what is happening in both cases is that there is ONE .gz file that is not a proper paired-end R1/R2 file in the sorted_fastq_path directory, and this is triggering the errors. It might help to be more specific about the exact files to use, like this:

./*_R*_*.gz ## [4] [sorted_fastq_path]: Location of demultiplexed/sorted fastq files

This will only include files with R* in the path, which should exclude any other non-paired files.

If you can show the full contents of the fastq directory it would help me figure out which file is causing this issue.

Cilia77 commented 2 months ago

Hello Isaac. Thank you for your reply. There is no error when I run only step1 in order to demultiplex my raw sequence data. I have a library with different samples that I first demultiplex and then analyse separately. Therefore I first run step1 and then use the demultiplexed sequences in different analyses.

The error that I get when I run S1to S7 using the demultiplexed data is:

ipyrad [v.0.9.96] Interactive assembly and analysis of RAD-seq data

Parallel connection | node0.cluster.nhmc.uoc.gr: 40 cores

Step 1: Loading sorted fastq data to Samples No PE fastq pairs detected based on filenames, assuming SE data. fastq file name (Ht_Gour4R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2, $ fastq file name (Ht_46R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2, or $ fastq file name (Ht_Gour1R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2, $ fastq file name (Ht_Dia5R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2, o$ fastq file name (Ht_92R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2, or $ fastq file name (Ht_Lyk3R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2, o$ fastq file name (Ht_Xerok4R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2,$ fastq file name (Ht_Plaka5R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2,$ fastq file name (Ht_Ofi6R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2, o$ fastq file name (Ht_Syros11R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2$ fastq file name (Ht_Syros12R2.fastq.gz) has a filename that suggests it may be an R2 read, but its paired R1 file could not be found. Paired files should have matching names except for _1 _2, _R1 _R2$ ... [####################] 100% 0:03:19 | loading reads
398 fastq files loaded to 199 Samples.

Step 2: Filtering and trimming reads [####################] 100% 0:00:17 | processing reads
199 Samples failed step 2. See /home/cilia/Macrogen/ddRAD/Ht/Hexaplex_edits/s2_error_log.txt for details.

Step 3: Clustering/Mapping reads within samples skipping samples not yet in state==2: ['Ht_100R1', 'Ht_100R2', 'Ht_10R1', 'Ht_10R2', 'Ht27 ... Encountered an Error. Message: No samples ready for step 3. If branching, use the -f flag to force re-running step 3. Parallel connection closed.

Please note that this is not happening with all samples that were demulptiplexed from the same library i.e. some samples of the library that have been demultiplexed in the same ipyrad step1 analysis are running fine.

You can see the full path to the fastqs directory and ls -l below: ls -l ~/Macrogen/ddRAD/Ht/ total 24181000 drwxr-xr-x 2 cilia nhmc 32768 Ιούλ 15 13:31 Hexaplex_edits -rw-r--r-- 1 cilia nhmc 604539 Ιούλ 15 13:31 Hexaplex.json -rw-r--r-- 1 cilia nhmc 5399 Ιούλ 15 13:30 Hexaplex_s1_demultiplex_stats.txt -rw-r--r-- 1 cilia nhmc 104767222 Ιούν 28 23:47 Ht_100R1.fastq.gz -rw-r--r-- 1 cilia nhmc 111808494 Ιούν 28 23:48 Ht_100R2.fastq.gz -rw-r--r-- 1 cilia nhmc 351054229 Ιούν 28 14:19 Ht_10R1.fastq.gz -rw-r--r-- 1 cilia nhmc 372804038 Ιούν 28 14:20 Ht_10R2.fastq.gz -rw-r--r-- 1 cilia nhmc 73944870 Ιούν 28 23:40 Ht_27R1.fastq.gz -rw-r--r-- 1 cilia nhmc 78718934 Ιούν 28 23:40 Ht_27R2.fastq.gz -rw-r--r-- 1 cilia nhmc 69323747 Ιούν 28 21:39 Ht_31R1.fastq.gz -rw-r--r-- 1 cilia nhmc 73678839 Ιούν 28 21:39 Ht_31R2.fastq.gz -rw-r--r-- 1 cilia nhmc 205936515 Ιούν 28 14:20 Ht_38R1.fastq.gz -rw-r--r-- 1 cilia nhmc 213987155 Ιούν 28 14:20 Ht_38R2.fastq.gz -rw-r--r-- 1 cilia nhmc 201912121 Ιούν 28 14:05 Ht_39R1.fastq.gz -rw-r--r-- 1 cilia nhmc 215968940 Ιούν 28 14:06 Ht_39R2.fastq.gz -rw-r--r-- 1 cilia nhmc 316240706 Ιούν 28 14:00 Ht_46R1.fastq.gz -rw-r--r-- 1 cilia nhmc 339062121 Ιούν 28 14:00 Ht_46R2.fastq.gz -rw-r--r-- 1 cilia nhmc 214612247 Ιούν 28 23:46 Ht_49R1.fastq.gz -rw-r--r-- 1 cilia nhmc 230636500 Ιούν 28 23:46 Ht_49R2.fastq.gz -rw-r--r-- 1 cilia nhmc 40383652 Ιούν 29 13:39 Ht_52R1.fastq.gz -rw-r--r-- 1 cilia nhmc 43490600 Ιούν 29 13:39 Ht_52R2.fastq.gz -rw-r--r-- 1 cilia nhmc 43751435 Ιούν 27 17:46 Ht_62R1.fastq.gz -rw-r--r-- 1 cilia nhmc 46300574 Ιούν 27 17:46 Ht_62R2.fastq.gz -rw-r--r-- 1 cilia nhmc 24675645 Ιούν 28 14:17 Ht_63R1.fastq.gz -rw-r--r-- 1 cilia nhmc 25677582 Ιούν 28 14:17 Ht_63R2.fastq.gz -rw-r--r-- 1 cilia nhmc 17596339 Ιούν 28 14:14 Ht_65R1.fastq.gz -rw-r--r-- 1 cilia nhmc 18340796 Ιούν 28 14:14 Ht_65R2.fastq.gz -rw-r--r-- 1 cilia nhmc 7611532 Ιούν 28 23:40 Ht_66R1.fastq.gz -rw-r--r-- 1 cilia nhmc 8142044 Ιούν 28 23:40 Ht_66R2.fastq.gz -rw-r--r-- 1 cilia nhmc 58148683 Ιούν 28 14:15 Ht_70R1.fastq.gz -rw-r--r-- 1 cilia nhmc 62153458 Ιούν 28 14:15 Ht_70R2.fastq.gz -rw-r--r-- 1 cilia nhmc 31524886 Ιούν 28 14:02 Ht_74R1.fastq.gz -rw-r--r-- 1 cilia nhmc 33664816 Ιούν 28 14:02 Ht_74R2.fastq.gz -rw-r--r-- 1 cilia nhmc 9904517 Ιούν 28 14:15 Ht_75R1.fastq.gz -rw-r--r-- 1 cilia nhmc 10527729 Ιούν 28 14:15 Ht_75R2.fastq.gz -rw-r--r-- 1 cilia nhmc 166480804 Ιούν 27 17:48 Ht_76R1.fastq.gz -rw-r--r-- 1 cilia nhmc 178142725 Ιούν 27 17:48 Ht_76R2.fastq.gz -rw-r--r-- 1 cilia nhmc 300274276 Ιούν 28 14:04 Ht_7R1.fastq.gz -rw-r--r-- 1 cilia nhmc 319792300 Ιούν 28 14:05 Ht_7R2.fastq.gz -rw-r--r-- 1 cilia nhmc 29131491 Ιούν 28 14:23 Ht_84R1.fastq.gz -rw-r--r-- 1 cilia nhmc 31073193 Ιούν 28 14:23 Ht_84R2.fastq.gz -rw-r--r-- 1 cilia nhmc 264965404 Ιούν 29 13:36 Ht_85R1.fastq.gz -rw-r--r-- 1 cilia nhmc 283881020 Ιούν 29 13:37 Ht_85R2.fastq.gz -rw-r--r-- 1 cilia nhmc 34063893 Ιούν 28 14:02 Ht_86R1.fastq.gz -rw-r--r-- 1 cilia nhmc 35551691 Ιούν 28 14:03 Ht_86R2.fastq.gz -rw-r--r-- 1 cilia nhmc 19927309 Ιούν 28 14:10 Ht_88R1.fastq.gz -rw-r--r-- 1 cilia nhmc 20869545 Ιούν 28 14:10 Ht_88R2.fastq.gz -rw-r--r-- 1 cilia nhmc 287490817 Ιούν 28 14:15 Ht_89R1.fastq.gz -rw-r--r-- 1 cilia nhmc 307937836 Ιούν 28 14:16 Ht_89R2.fastq.gz -rw-r--r-- 1 cilia nhmc 121938928 Ιούν 28 14:05 Ht_8R1.fastq.gz -rw-r--r-- 1 cilia nhmc 129826735 Ιούν 28 14:05 Ht_8R2.fastq.gz -rw-r--r-- 1 cilia nhmc 214772099 Ιούν 28 14:02 Ht_90R1.fastq.gz -rw-r--r-- 1 cilia nhmc 231308307 Ιούν 28 14:02 Ht_90R2.fastq.gz -rw-r--r-- 1 cilia nhmc 22900244 Ιούν 29 13:37 Ht_91R1.fastq.gz -rw-r--r-- 1 cilia nhmc 24372790 Ιούν 29 13:37 Ht_91R2.fastq.gz -rw-r--r-- 1 cilia nhmc 230202628 Ιούν 28 21:40 Ht_92R1.fastq.gz -rw-r--r-- 1 cilia nhmc 246997279 Ιούν 28 21:40 Ht_92R2.fastq.gz -rw-r--r-- 1 cilia nhmc 233953949 Ιούν 28 14:06 Ht_93R1.fastq.gz -rw-r--r-- 1 cilia nhmc 250192643 Ιούν 28 14:06 Ht_93R2.fastq.gz -rw-r--r-- 1 cilia nhmc 51747418 Ιούν 28 14:16 Ht_9R1.fastq.gz -rw-r--r-- 1 cilia nhmc 54653931 Ιούν 28 14:16 Ht_9R2.fastq.gz -rw-r--r-- 1 cilia nhmc 432232909 Ιούν 28 14:21 Ht_Ant1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 464986670 Ιούν 28 14:21 Ht_Ant1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 85803917 Ιούν 28 23:48 Ht_Ant2R1.fastq.gz -rw-r--r-- 1 cilia nhmc 91275642 Ιούν 28 23:49 Ht_Ant2R2.fastq.gz -rw-r--r-- 1 cilia nhmc 163299630 Ιούν 29 13:38 Ht_Chiona14R1.fastq.gz -rw-r--r-- 1 cilia nhmc 173679518 Ιούν 29 13:38 Ht_Chiona14R2.fastq.gz -rw-r--r-- 1 cilia nhmc 159499040 Ιούν 27 17:48 Ht_Chiona15R1.fastq.gz -rw-r--r-- 1 cilia nhmc 169258961 Ιούν 27 17:48 Ht_Chiona15R2.fastq.gz -rw-r--r-- 1 cilia nhmc 42202784 Ιούν 28 23:41 Ht_Chiona16R1.fastq.gz -rw-r--r-- 1 cilia nhmc 45239826 Ιούν 28 23:41 Ht_Chiona16R2.fastq.gz -rw-r--r-- 1 cilia nhmc 31495088 Ιούν 28 14:00 Ht_Chiona19R1.fastq.gz -rw-r--r-- 1 cilia nhmc 33787521 Ιούν 28 14:00 Ht_Chiona19R2.fastq.gz -rw-r--r-- 1 cilia nhmc 12939456 Ιούν 28 14:06 Ht_Chiona21R1.fastq.gz -rw-r--r-- 1 cilia nhmc 13699660 Ιούν 28 14:06 Ht_Chiona21R2.fastq.gz -rw-r--r-- 1 cilia nhmc 9338084 Ιούν 28 14:06 Ht_Chiona22R1.fastq.gz -rw-r--r-- 1 cilia nhmc 9851988 Ιούν 28 14:06 Ht_Chiona22R2.fastq.gz -rw-r--r-- 1 cilia nhmc 72820710 Ιούν 28 14:16 Ht_Chiona23R1.fastq.gz -rw-r--r-- 1 cilia nhmc 77513086 Ιούν 28 14:16 Ht_Chiona23R2.fastq.gz -rw-r--r-- 1 cilia nhmc 153526776 Ιούν 28 22:00 Ht_Dia4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 162312809 Ιούν 28 22:00 Ht_Dia4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 150016247 Ιούν 28 22:00 Ht_Dia5R1.fastq.gz -rw-r--r-- 1 cilia nhmc 158386707 Ιούν 28 22:00 Ht_Dia5R2.fastq.gz -rw-r--r-- 1 cilia nhmc 306335381 Ιούν 27 18:27 Ht_Dia6R1.fastq.gz -rw-r--r-- 1 cilia nhmc 327578908 Ιούν 27 18:28 Ht_Dia6R2.fastq.gz -rw-r--r-- 1 cilia nhmc 34932262 Ιούν 29 19:08 Ht_Ger1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 35966463 Ιούν 29 19:08 Ht_Ger1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 265658130 Ιούν 29 13:36 Ht_Gour1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 284518522 Ιούν 29 13:36 Ht_Gour1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 84102677 Ιούν 28 14:21 Ht_Gour3R1.fastq.gz -rw-r--r-- 1 cilia nhmc 89051851 Ιούν 28 14:22 Ht_Gour3R2.fastq.gz -rw-r--r-- 1 cilia nhmc 23722641 Ιούν 28 14:10 Ht_Gour4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 25443190 Ιούν 28 14:10 Ht_Gour4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 223958537 Ιούν 28 14:23 Ht_Gour5R1.fastq.gz -rw-r--r-- 1 cilia nhmc 239265514 Ιούν 28 14:23 Ht_Gour5R2.fastq.gz -rw-r--r-- 1 cilia nhmc 46928691 Ιούν 28 14:10 Ht_Gour6R1.fastq.gz -rw-r--r-- 1 cilia nhmc 50055520 Ιούν 28 14:10 Ht_Gour6R2.fastq.gz -rw-r--r-- 1 cilia nhmc 49427110 Ιούν 28 14:09 Ht_Ht31720.3R1.fastq.gz -rw-r--r-- 1 cilia nhmc 52844814 Ιούν 28 14:09 Ht_Ht31720.3R2.fastq.gz -rw-r--r-- 1 cilia nhmc 283793231 Ιούν 27 17:47 Ht_Ht31720.4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 302670499 Ιούν 27 17:47 Ht_Ht31720.4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 29628192 Ιούν 27 17:47 Ht_Ira1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 31834404 Ιούν 27 17:47 Ht_Ira1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 68083125 Ιούν 28 21:39 Ht_Ira4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 72602250 Ιούν 28 21:39 Ht_Ira4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 30999362 Ιούν 28 21:40 Ht_Ira5R1.fastq.gz -rw-r--r-- 1 cilia nhmc 33004259 Ιούν 28 21:40 Ht_Ira5R2.fastq.gz -rw-r--r-- 1 cilia nhmc 152536916 Ιούν 29 13:38 Ht_Kouf1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 164083111 Ιούν 29 13:38 Ht_Kouf1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 45020965 Ιούν 28 22:03 Ht_KoutsR1.fastq.gz -rw-r--r-- 1 cilia nhmc 47688480 Ιούν 28 22:04 Ht_KoutsR2.fastq.gz -rw-r--r-- 1 cilia nhmc 106383360 Ιούν 28 23:41 Ht_Lyg1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 114983051 Ιούν 28 23:41 Ht_Lyg1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 210899185 Ιούν 28 14:14 Ht_Lyg2R1.fastq.gz -rw-r--r-- 1 cilia nhmc 226531762 Ιούν 28 14:15 Ht_Lyg2R2.fastq.gz -rw-r--r-- 1 cilia nhmc 102113186 Ιούν 28 14:09 Ht_Lyg3R1.fastq.gz -rw-r--r-- 1 cilia nhmc 109392130 Ιούν 28 14:09 Ht_Lyg3R2.fastq.gz -rw-r--r-- 1 cilia nhmc 254667667 Ιούν 29 13:37 Ht_Lyg4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 267470215 Ιούν 29 13:38 Ht_Lyg4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 42946270 Ιούν 28 14:01 Ht_Lyg5R1.fastq.gz -rw-r--r-- 1 cilia nhmc 46386530 Ιούν 28 14:01 Ht_Lyg5R2.fastq.gz -rw-r--r-- 1 cilia nhmc 158200188 Ιούν 28 14:17 Ht_Lyk1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 168717958 Ιούν 28 14:17 Ht_Lyk1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 180759468 Ιούν 28 21:39 Ht_Lyk2R1.fastq.gz -rw-r--r-- 1 cilia nhmc 194099508 Ιούν 28 21:39 Ht_Lyk2R2.fastq.gz -rw-r--r-- 1 cilia nhmc 196961954 Ιούν 28 14:16 Ht_Lyk3R1.fastq.gz -rw-r--r-- 1 cilia nhmc 211765708 Ιούν 28 14:16 Ht_Lyk3R2.fastq.gz -rw-r--r-- 1 cilia nhmc 73114352 Ιούν 28 14:01 Ht_Lyk4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 78770012 Ιούν 28 14:01 Ht_Lyk4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 10757679 Ιούν 27 17:46 Ht_Moh1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 11191802 Ιούν 27 17:46 Ht_Moh1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 162919434 Ιούν 28 14:00 Ht_Moh2R1.fastq.gz -rw-r--r-- 1 cilia nhmc 174924222 Ιούν 28 14:01 Ht_Moh2R2.fastq.gz -rw-r--r-- 1 cilia nhmc 156699014 Ιούν 28 14:10 Ht_Naf12R1.fastq.gz -rw-r--r-- 1 cilia nhmc 167379240 Ιούν 28 14:10 Ht_Naf12R2.fastq.gz -rw-r--r-- 1 cilia nhmc 26488193 Ιούν 28 23:41 Ht_Naf13R1.fastq.gz -rw-r--r-- 1 cilia nhmc 28256074 Ιούν 28 23:41 Ht_Naf13R2.fastq.gz -rw-r--r-- 1 cilia nhmc 28509018 Ιούν 28 23:41 Ht_Naf14R1.fastq.gz -rw-r--r-- 1 cilia nhmc 30500213 Ιούν 28 23:41 Ht_Naf14R2.fastq.gz -rw-r--r-- 1 cilia nhmc 90285946 Ιούν 28 23:41 Ht_Ofi10R1.fastq.gz -rw-r--r-- 1 cilia nhmc 94364730 Ιούν 28 23:41 Ht_Ofi10R2.fastq.gz -rw-r--r-- 1 cilia nhmc 37529155 Ιούν 28 14:10 Ht_Ofi1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 40547843 Ιούν 28 14:10 Ht_Ofi1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 95125453 Ιούν 28 14:01 Ht_Ofi2R1.fastq.gz -rw-r--r-- 1 cilia nhmc 101704965 Ιούν 28 14:01 Ht_Ofi2R2.fastq.gz -rw-r--r-- 1 cilia nhmc 4929969 Ιούν 28 23:41 Ht_Ofi3R1.fastq.gz -rw-r--r-- 1 cilia nhmc 5311516 Ιούν 28 23:41 Ht_Ofi3R2.fastq.gz -rw-r--r-- 1 cilia nhmc 110187613 Ιούν 29 13:39 Ht_Ofi6R1.fastq.gz -rw-r--r-- 1 cilia nhmc 118062918 Ιούν 29 13:39 Ht_Ofi6R2.fastq.gz -rw-r--r-- 1 cilia nhmc 42375830 Ιούν 28 21:40 Ht_Pal1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 44836255 Ιούν 28 21:40 Ht_Pal1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 393149703 Ιούν 28 23:49 Ht_Pal3R1.fastq.gz -rw-r--r-- 1 cilia nhmc 411560069 Ιούν 28 23:50 Ht_Pal3R2.fastq.gz -rw-r--r-- 1 cilia nhmc 182293787 Ιούν 28 14:23 Ht_Pal4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 194892515 Ιούν 28 14:23 Ht_Pal4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 91663936 Ιούν 28 21:40 Ht_Pal5R1.fastq.gz -rw-r--r-- 1 cilia nhmc 97556180 Ιούν 28 21:41 Ht_Pal5R2.fastq.gz -rw-r--r-- 1 cilia nhmc 138287569 Ιούν 28 23:48 Ht_Pal7R1.fastq.gz -rw-r--r-- 1 cilia nhmc 146409247 Ιούν 28 23:48 Ht_Pal7R2.fastq.gz -rw-r--r-- 1 cilia nhmc 17532394 Ιούν 27 17:47 Ht_Plaka1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 18725980 Ιούν 27 17:47 Ht_Plaka1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 368410317 Ιούν 28 23:47 Ht_Plaka2R1.fastq.gz -rw-r--r-- 1 cilia nhmc 393894643 Ιούν 28 23:47 Ht_Plaka2R2.fastq.gz -rw-r--r-- 1 cilia nhmc 143372025 Ιούν 28 23:48 Ht_Plaka3R1.fastq.gz -rw-r--r-- 1 cilia nhmc 153174276 Ιούν 28 23:48 Ht_Plaka3R2.fastq.gz -rw-r--r-- 1 cilia nhmc 203563539 Ιούν 27 17:46 Ht_Plaka4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 217896419 Ιούν 27 17:46 Ht_Plaka4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 191599508 Ιούν 28 21:41 Ht_Plaka5R1.fastq.gz -rw-r--r-- 1 cilia nhmc 199609773 Ιούν 28 21:41 Ht_Plaka5R2.fastq.gz -rw-r--r-- 1 cilia nhmc 139902935 Ιούν 28 14:01 Ht_Sant1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 149041868 Ιούν 28 14:01 Ht_Sant1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 28027797 Ιούν 28 23:47 Ht_Syros10R1.fastq.gz -rw-r--r-- 1 cilia nhmc 29635662 Ιούν 28 23:47 Ht_Syros10R2.fastq.gz -rw-r--r-- 1 cilia nhmc 68792334 Ιούν 28 14:01 Ht_Syros11R1.fastq.gz -rw-r--r-- 1 cilia nhmc 73565561 Ιούν 28 14:01 Ht_Syros11R2.fastq.gz -rw-r--r-- 1 cilia nhmc 62745861 Ιούν 28 14:01 Ht_Syros12R1.fastq.gz -rw-r--r-- 1 cilia nhmc 67047287 Ιούν 28 14:01 Ht_Syros12R2.fastq.gz -rw-r--r-- 1 cilia nhmc 16744406 Ιούν 28 14:06 Ht_Syros13R1.fastq.gz -rw-r--r-- 1 cilia nhmc 17914588 Ιούν 28 14:06 Ht_Syros13R2.fastq.gz -rw-r--r-- 1 cilia nhmc 53049673 Ιούν 28 14:10 Ht_Syros1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 56254157 Ιούν 28 14:10 Ht_Syros1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 6206395 Ιούν 28 14:00 Ht_Syros2R1.fastq.gz -rw-r--r-- 1 cilia nhmc 6623041 Ιούν 28 14:00 Ht_Syros2R2.fastq.gz -rw-r--r-- 1 cilia nhmc 25871166 Ιούν 28 14:14 Ht_Syros3R1.fastq.gz -rw-r--r-- 1 cilia nhmc 27770729 Ιούν 28 14:14 Ht_Syros3R2.fastq.gz -rw-r--r-- 1 cilia nhmc 20371364 Ιούν 28 14:06 Ht_Syros4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 21157700 Ιούν 28 14:06 Ht_Syros4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 13709624 Ιούν 28 14:01 Ht_Syros6R1.fastq.gz -rw-r--r-- 1 cilia nhmc 14469873 Ιούν 28 14:01 Ht_Syros6R2.fastq.gz -rw-r--r-- 1 cilia nhmc 13249850 Ιούν 28 14:16 Ht_Syros7R1.fastq.gz -rw-r--r-- 1 cilia nhmc 14025279 Ιούν 28 14:16 Ht_Syros7R2.fastq.gz -rw-r--r-- 1 cilia nhmc 12390700 Ιούν 28 14:16 Ht_Syros8R1.fastq.gz -rw-r--r-- 1 cilia nhmc 13202119 Ιούν 28 14:16 Ht_Syros8R2.fastq.gz -rw-r--r-- 1 cilia nhmc 14108208 Ιούν 28 14:17 Ht_Syros9R1.fastq.gz -rw-r--r-- 1 cilia nhmc 14854776 Ιούν 28 14:17 Ht_Syros9R2.fastq.gz -rw-r--r-- 1 cilia nhmc 123277551 Ιούν 28 14:17 Ht_Xerok1R1.fastq.gz -rw-r--r-- 1 cilia nhmc 131444981 Ιούν 28 14:17 Ht_Xerok1R2.fastq.gz -rw-r--r-- 1 cilia nhmc 144663851 Ιούν 28 14:02 Ht_Xerok2R1.fastq.gz -rw-r--r-- 1 cilia nhmc 153483658 Ιούν 28 14:02 Ht_Xerok2R2.fastq.gz -rw-r--r-- 1 cilia nhmc 256033750 Ιούν 28 14:22 Ht_Xerok4R1.fastq.gz -rw-r--r-- 1 cilia nhmc 273501158 Ιούν 28 14:22 Ht_Xerok4R2.fastq.gz -rw-r--r-- 1 cilia nhmc 233718597 Ιούν 28 14:18 Ht_Xerok6R1.fastq.gz -rw-r--r-- 1 cilia nhmc 249425110 Ιούν 28 14:18 Ht_Xerok6R2.fastq.gz -rw-r--r-- 1 cilia nhmc 224221666 Ιούν 28 14:02 Ht_Xerok7R1.fastq.gz -rw-r--r-- 1 cilia nhmc 235099435 Ιούν 28 14:02 Ht_Xerok7R2.fastq.gz -rw-r--r-- 1 cilia nhmc 151737 Ιούλ 15 13:31 ipyrad_Sall.out -rw-r--r-- 1 cilia nhmc 813 Ιούλ 9 12:48 ipyrad_script.sh -rw-r--r-- 1 cilia nhmc 3043 Ιούλ 9 12:30 params-prasino.txt

The problem persists even when I am more specific on the file names . I also attach ipyrad's log/output files. [Uploading Hexaplex_s1_demultiplex_stats.txt…]()

Please let me know if you need any further details. Thank you! Cilia

isaacovercast commented 2 months ago

Thank you for sending this info. I have found the problem. The new code for loading fastq data from the sorted_fastqs_path doesn't like having periods ('.') in the sample name. I can fix this, but the easiest way to get you going would be to replace the periods in these four gz files with dashes or underscores:

Ht_Ht31720.3R1.fastq.gz Ht_Ht31720.3R2.fastq.gz Ht_Ht31720.4R1.fastq.gz Ht_Ht31720.4R2.fastq.gz

For example, like this (which I tried and it works):

Ht_Ht31720-3R1.fastq.gz Ht_Ht31720-3R2.fastq.gz Ht_Ht31720-4R1.fastq.gz Ht_Ht31720-4R2.fastq.gz

isaacovercast commented 2 months ago

Inside ipyrad.assemble.pair_fastqs.drop_from_right (L70):

chunks = path.name.split(delim)[::-1]

The Path.name() call considers anything following a '.' to be suffix, so path.name mangles the sample names that include periods.

Periods seem like reasonable characters to allow in sample names, so it's not immediately clear to me how to fix this.

Cilia77 commented 2 months ago

Yes that was the problem. I renamed the files removing '.' and now it is solved!!! Thank you so much for figuring this out and apologies for bothering you with such an issue. I usually do not use '.' because of the problems they cause and that is why I did not think of that in the first place. Best, Cilia

isaacovercast commented 2 months ago

Wonderful! It should work now: 1aa0e18b

The fix will go out in the next bioconda version (v0.9.97), which I will push some time in the near future. thanks for reporting it!