search

Transipedia / dekupl-run

Identify differentially expressed k-mers between RNA-Seq datasets
MIT License
11 stars 11 forks source link

segfault in joinCounts #72

Open timodonnell opened 3 years ago

timodonnell commented 3 years ago

I am running over a large number of samples (~400 paired end samples) and /dekupl/bin/joinCounts is exiting immediately with error code 139 (segfault). Have you hit this before? Any idea what might cause it or what a possible workaround would be?

This is on docker transipedia/dekupl-run:latest (d39c8cf...) - which I notice is 2 years old. Is there an updated docker image I should be using?

Many thanks - appreciate your work on this tool.

Tim

Error in rule join_counts:
    jobid: 0
    output: results/kmer_counts/raw-counts.tsv.gz
    log: results/Logs/joinRawCounts_exec_time.log

RuleException:
CalledProcessError in line 570 of /dekupl/Snakefile:
Command ' set -euo pipefail;  /dekupl/bin/joinCounts -r 2 -a 5 results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_TGACCA_L005.txt.gz results/kmer_counts/sample_130325_UNC12_SN629_0268_AC22W1ACXX_AGTTCC_L008.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_TTAGGC_L007.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0142
_BD0HK1ACXX_CTTGTA_L006.txt.gz results/kmer_counts/sample_130702_UNC9_SN296_0379_AC25KWACXX_GATCAG_L008.txt.gz results/kmer_counts/sample_130517_UNC9_SN296_0365_AD24UDACXX_GTGGCC_L002.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_ACAGTG_L005.txt.gz results/kmer_counts/sample_140603_UNC15_SN850_0368_AC4GHHACXX_TTAGGC_L002.txt.gz res
ults/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_ATCACG_L003.txt.gz results/kmer_counts/sample_130325_UNC12_SN629_0268_AC22W1ACXX_GTGGCC_L004.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_GATCAG_L007.txt.gz results/kmer_counts/sample_120207_UNC10_SN254_0325_AC0C6MACXX_TGACCA_L006.txt.gz results/kmer_counts/sample_141010_U
NC12_SN629_0395_BC5FVEACXX_CAGATC_L001.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_CGATGT_L001.txt.gz results/kmer_counts/sample_130807_UNC12_SN629_0325_BD2BD7ACXX_GGCTAC_L002.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0360_AC4H72ACXX_GCCAAT_L008.txt.gz results/kmer_counts/sample_130814_UNC10_SN254_0487_AC2BD1ACXX_CAGAT
C_L006.txt.gz results/kmer_counts/sample_120124_UNC16_SN851_0123_AC0FDJACXX_ACTTGA_L006.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_CTTGTA_L001.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_GGCTAC_L002.txt.gz results/kmer_counts/sample_131008_UNC11_SN627_0326_AC2KLPACXX_CAGATC_L001.txt.gz results/kmer_count
s/sample_120723_UNC10_SN254_0372_AC0T70ACXX_TTAGGC_L003.txt.gz results/kmer_counts/sample_121126_UNC9_SN296_0314_BC11Y0ACXX_GAGTGG_L005.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_GATCAG_L002.txt.gz results/kmer_counts/sample_131217_UNC14_SN744_0384_BC32YDACXX_TTAGGC_L003.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_
AC0UKHACXX_CAGATC_L008.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0142_BD0HK1ACXX_ACAGTG_L002.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_GATCAG_L008.txt.gz results/kmer_counts/sample_120723_UNC10_SN254_0372_AC0T70ACXX_TTAGGC_L001.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0142_BD0HK1ACXX_ACTTGA_L003.txt.gz re
sults/kmer_counts/sample_130227_UNC9_SN296_0341_AC1RM4ACXX_GATCAG_L006.txt.gz results/kmer_counts/sample_120124_UNC16_SN851_0123_AC0FDJACXX_GGCTAC_L008.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_GATCAG_L004.txt.gz results/kmer_counts/sample_140603_UNC15_SN850_0368_AC4GHHACXX_CGATGT_L001.txt.gz results/kmer_counts/sample_120508_U
NC15_SN850_0202_AC0UKHACXX_CTTGTA_L003.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0142_BD0HK1ACXX_TGACCA_L005.txt.gz results/kmer_counts/sample_140417_UNC13_SN749_0342_AC41N6ACXX_CTTGTA_L007.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_ACAGTG_L001.txt.gz results/kmer_counts/sample_131217_UNC14_SN744_0384_BC32YDACXX_ACAGT
G_L006.txt.gz results/kmer_counts/sample_140924_UNC15_SN850_0394_AC5DG0ACXX_CAGATC_L008.txt.gz results/kmer_counts/sample_140417_UNC13_SN749_0343_BC41HBACXX_GGCTAC_L007.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_AGTCAA_L006.txt.gz results/kmer_counts/sample_131008_UNC15_SN850_0331_AC2KJ8ACXX_CAGATC_L006.txt.gz results/kmer_count
s/sample_120409_UNC14_SN744_0226_AC0M8NACXX_ATCACG_L006.txt.gz results/kmer_counts/sample_130402_UNC11_SN627_0289_AD22HMACXX_ATCACG_L001.txt.gz results/kmer_counts/sample_140312_UNC15_SN850_0357_AC3M7FACXX_ACAGTG_L005.txt.gz results/kmer_counts/sample_120207_UNC10_SN254_0325_AC0C6MACXX_GGCTAC_L007.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0394
_AC5FTUACXX_GCCAAT_L001.txt.gz results/kmer_counts/sample_130711_UNC12_SN629_0319_AC287CACXX_GTGGCC_L001.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_CTTGTA_L005.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_CAGATC_L002.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_ATCACG_L002.txt.gz r
esults/kmer_counts/sample_141006_UNC15_SN850_0395_AC5FH9ACXX_ACAGTG_L008.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0142_BD0HK1ACXX_GCCAAT_L001.txt.gz results/kmer_counts/sample_130702_UNC9_SN296_0380_BC24VKACXX_GATCAG_L006.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_CTTGTA_L003.txt.gz results/kmer_counts/sample_140617_
UNC11_SN627_0363_AC4HN7ACXX_GTTTCG_L003.txt.gz results/kmer_counts/sample_140603_UNC15_SN850_0368_AC4GHHACXX_AGTTCC_L006.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_GCCAAT_L001.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_GATCAG_L004.txt.gz results/kmer_counts/sample_130402_UNC11_SN627_0289_AD22HMACXX_TAGC
TT_L001.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0395_BC5FVEACXX_TTAGGC_L008.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_GTGGCC_L006.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_CGATGT_L006.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_GGCTAC_L002.txt.gz results/kmer_coun
ts/sample_130227_UNC9_SN296_0341_AC1RM4ACXX_GGCTAC_L004.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_GCCAAT_L004.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_CGTACG_L002.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_CGATGT_L008.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0365
_BC4BYLACXX_ATGTCA_L007.txt.gz results/kmer_counts/sample_121211_UNC16_SN851_0198_AD1KNMACXX_TAGCTT_L006.txt.gz results/kmer_counts/sample_130807_UNC12_SN629_0325_BD2BD7ACXX_ACTTGA_L003.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_TTAGGC_L008.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_TTAGGC_L006.txt.gz r
esults/kmer_counts/sample_140908_UNC11_SN627_0381_BC5DEKACXX_ATGTCA_L006.txt.gz results/kmer_counts/sample_130702_UNC9_SN296_0379_AC25KWACXX_GTTTCG_L006.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_AGTCAA_L004.txt.gz results/kmer_counts/sample_120207_UNC10_SN254_0325_AC0C6MACXX_TAGCTT_L008.txt.gz results/kmer_counts/sample_140603_
UNC11_SN627_0361_BC4K54ACXX_CGTACG_L008.txt.gz results/kmer_counts/sample_140908_UNC11_SN627_0381_BC5DEKACXX_AGTTCC_L005.txt.gz results/kmer_counts/sample_130325_UNC12_SN629_0268_AC22W1ACXX_GTTTCG_L005.txt.gz results/kmer_counts/sample_141006_UNC15_SN850_0395_AC5FH9ACXX_GTGAAA_L008.txt.gz results/kmer_counts/sample_130513_UNC14_SN744_0340_BD250CACXX_GGCT
AC_L003.txt.gz results/kmer_counts/sample_121211_UNC16_SN851_0198_AD1KNMACXX_ACTTGA_L006.txt.gz results/kmer_counts/sample_110426_UNC12_SN629_0077.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_CGATGT_L005.txt.gz results/kmer_counts/sample_121126_UNC9_SN296_0314_BC11Y0ACXX_TGACCA_L007.txt.gz results/kmer_counts/sample_140513_UNC15_S
N850_0365_BC4BYLACXX_CCGTCC_L003.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_ACTTGA_L003.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_GGCTAC_L003.txt.gz results/kmer_counts/sample_121211_UNC16_SN851_0198_AD1KNMACXX_GTGGCC_L005.txt.gz results/kmer_counts/sample_130325_UNC12_SN629_0268_AC22W1ACXX_GGCTAC_L007
.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0365_BC4BYLACXX_ACAGTG_L004.txt.gz results/kmer_counts/sample_130227_UNC9_SN296_0341_AC1RM4ACXX_GTTTCG_L004.txt.gz results/kmer_counts/sample_121126_UNC9_SN296_0314_BC11Y0ACXX_ACTGAT_L006.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_GGCTAC_L002.txt.gz results/kmer_counts/sample
_140513_UNC15_SN850_0364_AC4DVGACXX_CCGTCC_L006.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_TGACCA_L002.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_ACAGTG_L008.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_GTCCGC_L007.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7A
CXX_CCGTCC_L001.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_GAGTGG_L005.txt.gz results/kmer_counts/sample_130328_UNC10_SN254_0443_AD238RACXX_GTGGCC_L002.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0365_BC4BYLACXX_GCCAAT_L005.txt.gz results/kmer_counts/sample_131008_UNC15_SN850_0331_AC2KJ8ACXX_GCCAAT_L005.txt.gz results/k
mer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_CCGTCC_L004.txt.gz results/kmer_counts/sample_120207_UNC9_SN296_0271_BC0CB8ACXX_GCCAAT_L002.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_TTAGGC_L001.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_GGCTAC_L008.txt.gz results/kmer_counts/sample_140908_UNC11_SN
627_0381_BC5DEKACXX_GTCCGC_L001.txt.gz results/kmer_counts/sample_130702_UNC12_SN629_0318_BC25TVACXX_GCCAAT_L005.txt.gz results/kmer_counts/sample_120723_UNC10_SN254_0372_AC0T70ACXX_TTAGGC_L004.txt.gz results/kmer_counts/sample_130513_UNC14_SN744_0340_BD250CACXX_TAGCTT_L004.txt.gz results/kmer_counts/sample_120207_UNC9_SN296_0271_BC0CB8ACXX_CAGATC_L001.txt.gz results/kmer_counts/sample_140304_UNC14_SN744_0400_AC3LWGACXX_ATGTCA_L008.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_GCCAAT_L002.txt.gz results/kmer_counts/sample_140417_UNC13_SN749_0342_AC41N6ACXX_CGATGT_L005.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_TGACCA_L002.txt.gz results/kmer_counts/sample_130807_UNC12_SN629_0325_BD2BD7ACXX_GTTTCG_L003.txt.gz results/kmer_counts/sample_140625_UNC11_SN627_0364_AC4HLGACXX_GCCAAT_L001.txt.gz results/kmer_counts/sample_140312_UNC11_SN627_0348_AC3KRYACXX_ACTTGA_L005.txt.gz results/kmer_counts/sample_140304_UNC14_SN744_0400_AC3LWGACXX_ACTGAT_L007.txt.gz results/kmer_counts/sample_140508_UNC12_SN629_0367_AC3U9RACXX_ACTTGA_L007.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_AGTCAA_L005.txt.gz results/kmer_counts/sample_120207_UNC9_SN296_0271_BC0CB8ACXX_ACAGTG_L002.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0394_AC5FTUACXX_ATGTCA_L005.txt.gz results/kmer_counts/sample_130926_SN254_0496_AD2DY9ACXX_GATCAG_L001.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_ACTTGA_L004.txt.gz results/kmer_counts/sample_121211_UNC16_SN851_0198_AD1KNMACXX_ATCACG_L007.txt.gz results/kmer_counts/sample_140305_UNC13_SN749_0334_BC3L6VACXX_ATTCCT_L008.txt.gz results/kmer_counts/sample_140908_UNC11_SN627_0381_BC5DEKACXX_CCGTCC_L006.txt.gz results/kmer_counts/sample_140603_UNC15_SN850_0368_AC4GHHACXX_ATGTCA_L007.txt.gz results/kmer_counts/sample_140908_UNC11_SN627_0381_BC5DEKACXX_GTGGCC_L007.txt.gz results/kmer_counts/sample_130702_UNC9_SN296_0380_BC24VKACXX_GGCTAC_L001.txt.gz results/kmer_counts/sample_110725_UNC14_SN744_0149.txt.gz results/kmer_counts/sample_121211_UNC16_SN851_0198_AD1KNMACXX_TAGCTT_L008.txt.gz results/kmer_counts/sample_130827_UNC15_SN850_0324_AC2B28ACXX_CAGATC_L003.txt.gz results/kmer_counts/sample_120124_UNC16_SN851_0124_BC0C16ACXX_TGACCA_L004.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_ATTCCT_L003.txt.gz results/kmer_counts/sample_120514_UNC16_SN851_0159_BC0TARACXX_TTAGGC_L001.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_CGATGT_L002.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_TTAGGC_L006.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_CAGATC_L002.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_ACAGTG_L008.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_TTAGGC_L005.txt.gz results/kmer_counts/sample_130702_UNC9_SN296_0380_BC24VKACXX_GTTTCG_L001.txt.gz results/kmer_counts/sample_140924_UNC15_SN850_0394_AC5DG0ACXX_CGATGT_L007.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0142_BD0HK1ACXX_GCCAAT_L008.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_CTTGTA_L003.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0395_BC5FVEACXX_GCCAAT_L001.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_GTGAAA_L002.txt.gz results/kmer_counts/sample_140603_UNC15_SN850_0368_AC4GHHACXX_CTTGTA_L004.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_ATCACG_L004.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0395_BC5FVEACXX_TGACCA_L008.txt.gz results/kmer_counts/sample_130402_UNC11_SN627_0289_AD22HMACXX_TTAGGC_L003.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_ACTTGA_L004.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_ATCACG_L006.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0394_AC5FTUACXX_GTGGCC_L004.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_GATCAG_L008.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_ACAGTG_L005.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_CGTACG_L002.txt.gz results/kmer_counts/sample_140508_UNC11_SN627_0356_AC3UKNACXX_GTGGCC_L005.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_ACTGAT_L006.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_CAGATC_L002.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_GTTTCG_L007.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_GGCTAC_L004.txt.gz results/kmer_counts/sample_130702_UNC9_SN296_0380_BC24VKACXX_ATCACG_L008.txt.gz results/kmer_counts/sample_130402_UNC11_SN627_0289_AD22HMACXX_ACTTGA_L002.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0395_BC5FVEACXX_ACAGTG_L008.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_GGCTAC_L003.txt.gz results/kmer_counts/sample_130513_UNC14_SN744_0340_BD250CACXX_TTAGGC_L007.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_GCCAAT_L004.txt.gz results/kmer_counts/sample_130402_UNC11_SN627_0289_AD22HMACXX_GATCAG_L004.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_ACTTGA_L006.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_GATCAG_L004.txt.gz results/kmer_counts/sample_140617_UNC12_SN629_0374_AC4KA5ACXX_ATCACG_L008.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_ACAGTG_L002.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_CTTGTA_L003.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_TGACCA_L008.txt.gz results/kmer_counts/sample_130513_UNC14_SN744_0340_BD250CACXX_GGCTAC_L005.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_CAGATC_L006.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_CTTGTA_L005.txt.gz results/kmer_counts/sample_120207_UNC10_SN254_0325_AC0C6MACXX_CGATGT_L006.txt.gz results/kmer_counts/sample_140417_UNC13_SN749_0343_BC41HBACXX_ATTCCT_L005.txt.gz results/kmer_counts/sample_130513_UNC14_SN744_0340_BD250CACXX_GTGGCC_L008.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_TTAGGC_L001.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_CAGATC_L005.txt.gz results/kmer_counts/sample_131008_UNC11_SN627_0326_AC2KLPACXX_ACAGTG_L001.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_GATCAG_L006.txt.gz results/kmer_counts/sample_120207_UNC10_SN254_0325_AC0C6MACXX_ACTTGA_L007.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_ATCACG_L007.txt.gz results/kmer_counts/sample_130807_UNC12_SN629_0325_BD2BD7ACXX_GTGGCC_L005.txt.gz results/kmer_counts/sample_140603_UNC15_SN850_0368_AC4GHHACXX_GGCTAC_L005.txt.gz results/kmer_counts/sample_120124_UNC16_SN851_0124_BC0C16ACXX_CAGATC_L008.txt.gz results/kmer_counts/sample_131127_UNC15_SN850_0341_BC34HHACXX_TGACCA_L007.txt.gz results/kmer_counts/sample_141006_UNC15_SN850_0395_AC5FH9ACXX_ATGTCA_L004.txt.gz results/kmer_counts/sample_140617_UNC12_SN629_0374_AC4KA5ACXX_TTAGGC_L008.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_ACAGTG_L001.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0394_AC5FTUACXX_GTCCGC_L005.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_CGATGT_L006.txt.gz results/kmer_counts/sample_131127_UNC15_SN850_0341_BC34HHACXX_TTAGGC_L001.txt.gz results/kmer_counts/sample_140417_UNC13_SN749_0343_BC41HBACXX_ACTGAT_L004.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_TTAGGC_L002.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0365_BC4BYLACXX_TTAGGC_L003.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0365_BC4BYLACXX_ATCACG_L001.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_GATCAG_L008.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_GTGGCC_L007.txt.gz results/kmer_counts/sample_141006_UNC15_SN850_0395_AC5FH9ACXX_CGATGT_L007.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_TTAGGC_L003.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_ATCACG_L005.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_AGTCAA_L006.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_ACTTGA_L002.txt.gz results/kmer_counts/sample_121126_UNC9_SN296_0314_BC11Y0ACXX_GCCAAT_L008.txt.gz results/kmer_counts/sample_130718_UNC12_SN629_0321_AC2E6WACXX_ATGTCA_L007.txt.gz results/kmer_counts/sample_130325_UNC12_SN629_0268_AC22W1ACXX_GATCAG_L004.txt.gz results/kmer_counts/sample_131127_UNC15_SN850_0341_BC34HHACXX_GCCAAT_L006.txt.gz results/kmer_counts/sample_120207_UNC10_SN254_0325_AC0C6MACXX_GATCAG_L008.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_TAGCTT_L003.txt.gz results/kmer_counts/sample_131217_UNC14_SN744_0384_BC32YDACXX_ACAGTG_L007.txt.gz results/kmer_counts/sample_120124_UNC16_SN851_0124_BC0C16ACXX_ACAGTG_L006.txt.gz results/kmer_counts/sample_130513_UNC14_SN744_0340_BD250CACXX_GGCTAC_L008.txt.gz results/kmer_counts/sample_131016_UNC10_SN254_0498_BC2KTUACXX_GATCAG_L002.txt.gz results/kmer_counts/sample_120207_UNC9_SN296_0271_BC0CB8ACXX_CTTGTA_L003.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_ATGTCA_L004.txt.gz results/kmer_counts/sample_130529_UNC9_SN296_0368_AD24URACXX_GATCAG_L005.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_TGACCA_L001.txt.gz results/kmer_counts/sample_130702_UNC9_SN296_0380_BC24VKACXX_ACTTGA_L007.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_ATCACG_L008.txt.gz results/kmer_counts/sample_140521_UNC13_SN749_0354_BC4GJ7ACXX_ATCACG_L005.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_AGTTCC_L005.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_TAGCTT_L007.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_TGACCA_L004.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_TGACCA_L005.txt.gz results/kmer_counts/sample_130711_UNC12_SN629_0319_AC287CACXX_GTGGCC_L005.txt.gz results/kmer_counts/sample_130711_UNC12_SN629_0319_AC287CACXX_TAGCTT_L001.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_ATCACG_L001.txt.gz results/kmer_counts/sample_130513_UNC14_SN744_0340_BD250CACXX_GTGGCC_L002.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_CGATGT_L001.txt.gz results/kmer_counts/sample_140617_UNC12_SN629_0374_AC4KA5ACXX_CGATGT_L002.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0394_AC5FTUACXX_CCGTCC_L004.txt.gz results/kmer_counts/sample_131016_UNC15_SN850_0333_AC2MBAACXX_GATCAG_L007.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_ACAGTG_L008.txt.gz results/kmer_counts/sample_131008_UNC15_SN850_0331_AC2KJ8ACXX_CAGATC_L007.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_TTAGGC_L001.txt.gz results/kmer_counts/sample_120723_UNC10_SN254_0372_AC0T70ACXX_ATCACG_L002.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_GGCTAC_L002.txt.gz results/kmer_counts/sample_130702_UNC9_SN296_0380_BC24VKACXX_TTAGGC_L001.txt.gz results/kmer_counts/sample_130718_UNC12_SN629_0321_AC2E6WACXX_CTTGTA_L006.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_TAGCTT_L007.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_CAGATC_L004.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_ATGTCA_L007.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_TAGCTT_L004.txt.gz results/kmer_counts/sample_130513_UNC14_SN744_0340_BD250CACXX_GGCTAC_L001.txt.gz results/kmer_counts/sample_130227_UNC9_SN296_0341_AC1RM4ACXX_TTAGGC_L005.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_ACTTGA_L006.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_CCGTCC_L008.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_GGCTAC_L008.txt.gz results/kmer_counts/sample_141006_UNC15_SN850_0395_AC5FH9ACXX_GTCCGC_L005.txt.gz results/kmer_counts/sample_140312_UNC15_SN850_0357_AC3M7FACXX_AGTCAA_L008.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_TGACCA_L003.txt.gz results/kmer_counts/sample_131008_UNC15_SN850_0331_AC2KJ8ACXX_GCCAAT_L008.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0394_AC5FTUACXX_AGTTCC_L004.txt.gz results/kmer_counts/sample_140625_UNC11_SN627_0364_AC4HLGACXX_CAGATC_L002.txt.gz results/kmer_counts/sample_131127_UNC15_SN850_0341_BC34HHACXX_ATCACG_L005.txt.gz results/kmer_counts/sample_140424_UNC13_SN749_0344_AC3WUKACXX_CGTACG_L002.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_ATTCCT_L008.txt.gz results/kmer_counts/sample_130328_UNC10_SN254_0443_AD238RACXX_CTTGTA_L002.txt.gz results/kmer_counts/sample_140924_UNC15_SN850_0394_AC5DG0ACXX_TTAGGC_L007.txt.gz results/kmer_counts/sample_140924_UNC15_SN850_0394_AC5DG0ACXX_GCCAAT_L008.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_CTTGTA_L002.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0365_BC4BYLACXX_TGACCA_L001.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0395_BC5FVEACXX_CCGTCC_L004.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_CGATGT_L002.txt.gz results/kmer_counts/sample_130517_UNC9_SN296_0365_AD24UDACXX_GGCTAC_L003.txt.gz results/kmer_counts/sample_121126_UNC9_SN296_0314_BC11Y0ACXX_CAGATC_L004.txt.gz results/kmer_counts/sample_130118_UNC12_SN629_0249_AD1MRDACXX_GTGAAA_L007.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0365_BC4BYLACXX_AGTCAA_L003.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_ACAGTG_L005.txt.gz results/kmer_counts/sample_121126_UNC9_SN296_0314_BC11Y0ACXX_CGTACG_L005.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_TAGCTT_L001.txt.gz results/kmer_counts/sample_120723_UNC10_SN254_0372_AC0T70ACXX_ACTTGA_L004.txt.gz results/kmer_counts/sample_140424_UNC13_SN749_0344_AC3WUKACXX_GAGTGG_L002.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_GCCAAT_L002.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_GAGTGG_L005.txt.gz results/kmer_counts/sample_120409_UNC14_SN744_0226_AC0M8NACXX_TAGCTT_L003.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_CCGTCC_L006.txt.gz results/kmer_counts/sample_120508_UNC15_SN850_0202_AC0UKHACXX_TAGCTT_L002.txt.gz results/kmer_counts/sample_120207_UNC9_SN296_0271_BC0CB8ACXX_ATCACG_L003.txt.gz results/kmer_counts/sample_130325_UNC12_SN629_0268_AC22W1ACXX_GTTTCG_L002.txt.gz results/kmer_counts/sample_121211_UNC16_SN851_0198_AD1KNMACXX_ATCACG_L005.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_TGACCA_L006.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_CAGATC_L002.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0394_AC5FTUACXX_GTGAAA_L001.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0142_BD0HK1ACXX_CGATGT_L005.txt.gz results/kmer_counts/sample_120717_UNC14_SN744_0245_AC0WYWACXX_ACTTGA_L006.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_AGTTCC_L006.txt.gz results/kmer_counts/sample_121126_UNC9_SN296_0314_BC11Y0ACXX_ATTCCT_L006.txt.gz results/kmer_counts/sample_130402_UNC11_SN627_0289_AD22HMACXX_GTTTCG_L003.txt.gz results/kmer_counts/sample_140521_UNC11_SN627_0359_BC4E01ACXX_ACAGTG_L003.txt.gz results/kmer_counts/sample_120723_UNC10_SN254_0372_AC0T70ACXX_TAGCTT_L003.txt.gz results/kmer_counts/sample_140603_UNC15_SN850_0368_AC4GHHACXX_TGACCA_L002.txt.gz results/kmer_counts/sample_130807_UNC12_SN629_0325_BD2BD7ACXX_ATCACG_L005.txt.gz results/kmer_counts/sample_140611_UNC11_SN627_0362_BC4K5NACXX_ATGTCA_L005.txt.gz results/kmer_counts/sample_120110_UNC13_SN749_0141_AD0J7WACXX_CAGATC_L006.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_GGCTAC_L003.txt.gz results/kmer_counts/sample_140513_UNC15_SN850_0364_AC4DVGACXX_GTCCGC_L001.txt.gz results/kmer_counts/sample_120118_UNC12_SN629_0180_BC0BWMACXX_ACAGTG_L001.txt.gz results/kmer_counts/sample_131127_UNC15_SN850_0341_BC34HHACXX_TGACCA_L002.txt.gz results/kmer_counts/sample_131210_UNC12_SN629_0339_AC2UJ6ACXX_TGACCA_L006.txt.gz results/kmer_counts/sample_140603_UNC15_SN850_0368_AC4GHHACXX_AGTCAA_L004.txt.gz results/kmer_counts/sample_140617_UNC11_SN627_0363_AC4HN7ACXX_ATCACG_L005.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_GTGAAA_L001.txt.gz results/kmer_counts/sample_120724_UNC14_SN744_0249_AC0T3HACXX_TAGCTT_L007.txt.gz results/kmer_counts/sample_121211_UNC16_SN851_0198_AD1KNMACXX_GTGGCC_L007.txt.gz results/kmer_counts/sample_130325_UNC12_SN629_0268_AC22W1ACXX_TAGCTT_L004.txt.gz results/kmer_counts/sample_130517_UNC9_SN296_0365_AD24UDACXX_GTGGCC_L004.txt.gz results/kmer_counts/sample_141030_UNC15_SN850_0397_AC5F8LACXX_GTGAAA_L001.txt.gz results/kmer_counts/sample_141010_UNC12_SN629_0394_AC5FTUACXX_TTAGGC_L008.txt.gz results/kmer_counts/sample_121126_UNC9_SN296_0314_BC11Y0ACXX_CGATGT_L007.txt.gz results/kmer_counts/sample_120207_UNC10_SN254_0325_AC0C6MACXX_TTAGGC_L005.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_TAGCTT_L003.txt.gz results/kmer_counts/sample_140603_UNC11_SN627_0361_BC4K54ACXX_TTAGGC_L008.txt.gz results/kmer_counts/sample_130402_UNC11_SN627_0289_AD22HMACXX_GATCAG_L002.txt.gz | gzip -c >> results/kmer_counts/raw-counts.tsv.gz ' returned non-zero exit status 139.
  File "/dekupl/Snakefile", line 570, in __rule_join_counts
  File "/usr/local/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Exiting because a job execution failed. Look above for error message
aLaine1 commented 3 years ago

Hello Tim, I'm sorry to hear about the issue. There is actually an newer version of the tool which was released 10 months ago (1.3.5). For some reasons, it wasn't tagged as latest (it is now that i corrected it). Please let me know if the issue remains with the newest version.

Antoine

timodonnell commented 3 years ago

Thanks Antoine. I'm rerunning everything now with the new version, will let you know how it goes.

timodonnell commented 3 years ago

It's still running now, but I'm am noticing many invocations like this:

command line - /usr/local/lib/python3.6/site-packages/pulp/apis/../solverdir/cbc/linux/64/cbc /tmp/983e48dce38b481aba1a515cf2959a22-pulp.mps max ratio None allow None threads None presolve on strong None gomory on knapsack on probing on branch printingOptions all solution /tmp/983e48dce38b481aba1a515cf2959a22-pulp.sol (default strategy 1)
At line 2 NAME          MODEL
At line 3 ROWS
At line 7 COLUMNS
At line 13 RHS
At line 16 BOUNDS
At line 18 ENDATA
Problem MODEL has 2 rows, 1 columns and 2 elements
Coin0008I MODEL read with 0 errors
String of None is illegal for double parameter ratioGap value remains 0
String of None is illegal for double parameter allowableGap value remains 0
String of None is illegal for integer parameter threads value remains 0
String of None is illegal for integer parameter strongBranching value remains 5
Option for gomoryCuts changed from ifmove to on
Option for knapsackCuts changed from ifmove to on
Continuous objective value is 11 - 0.00 seconds
Cgl0004I processed model has 0 rows, 0 columns (0 integer (0 of which binary)) and 0 elements
Cbc3007W No integer variables - nothing to do
Cuts at root node changed objective from -11 to -1.79769e+308
Probing was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Gomory was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Knapsack was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
Clique was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
MixedIntegerRounding2 was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
FlowCover was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)
TwoMirCuts was tried 0 times and created 0 cuts of which 0 were active after adding rounds of cuts (0.000 seconds)

Result - Optimal solution found

Objective value:                11.00000000
Enumerated nodes:               0
Total iterations:               0
Time (CPU seconds):             0.00
Time (Wallclock seconds):       0.00

Option for printingOptions changed from normal to all
Total time (CPU seconds):       0.00   (Wallclock seconds):       0.00

This looks suspect having the Nones in the command-line, and the zero iterations. I looked in the Snakefile but couldn't easily see where this is happening. Curious what step uses a knapsack solver?

Anyway, just mentioning in case you spot an issue. Will update when the run has completed.