Job ID = 16436157 SRX = SRX9091669 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Warning: skipping mate #1 of read 'SRR12608190.26280346 26280346 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608190.26280346 26280346 length=1' because it was < 2 characters long Warning: skipping mate #1 of read 'SRR12608190.33254512 33254512 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #2 of read 'SRR12608190.33254512 33254512 length=1' because length (1) <= # seed mismatches (0) Warning: skipping mate #1 of read 'SRR12608190.33254512 33254512 length=1' because it was < 2 characters long Warning: skipping mate #2 of read 'SRR12608190.33254512 33254512 length=1' because it was < 2 characters long Error, fewer reads in file specified with -1 than in file specified with -2 terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 48 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 52742165 / 55999918 = 0.9418 in library ' ' awk: cmd. line:1: (FILENAME=- FNR=1) fatal: division by zero attempted BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:16:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 12:16:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:16:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:16:56: 1000000 INFO @ Tue, 02 Aug 2022 12:17:02: 2000000 INFO @ Tue, 02 Aug 2022 12:17:07: 3000000 INFO @ Tue, 02 Aug 2022 12:17:13: 4000000 INFO @ Tue, 02 Aug 2022 12:17:18: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:17:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 12:17:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:17:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:17:24: 6000000 INFO @ Tue, 02 Aug 2022 12:17:27: 1000000 INFO @ Tue, 02 Aug 2022 12:17:30: 7000000 INFO @ Tue, 02 Aug 2022 12:17:32: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:17:32: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:17:32: #1 total tags in treatment: 3264946 INFO @ Tue, 02 Aug 2022 12:17:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:17:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:17:32: #1 tags after filtering in treatment: 2735809 INFO @ Tue, 02 Aug 2022 12:17:32: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 12:17:32: #1 finished! INFO @ Tue, 02 Aug 2022 12:17:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:17:32: #2 number of paired peaks: 1243 INFO @ Tue, 02 Aug 2022 12:17:32: start model_add_line... INFO @ Tue, 02 Aug 2022 12:17:32: start X-correlation... INFO @ Tue, 02 Aug 2022 12:17:32: end of X-cor INFO @ Tue, 02 Aug 2022 12:17:32: #2 finished! INFO @ Tue, 02 Aug 2022 12:17:32: #2 predicted fragment length is 151 bps INFO @ Tue, 02 Aug 2022 12:17:32: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 02 Aug 2022 12:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.05_model.r INFO @ Tue, 02 Aug 2022 12:17:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:17:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:17:33: 2000000 INFO @ Tue, 02 Aug 2022 12:17:39: 3000000 INFO @ Tue, 02 Aug 2022 12:17:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:17:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:17:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:17:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.05_summits.bed INFO @ Tue, 02 Aug 2022 12:17:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (874 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:17:45: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:17:50: 5000000 INFO @ Tue, 02 Aug 2022 12:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 02 Aug 2022 12:17:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:17:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:17:57: 6000000 INFO @ Tue, 02 Aug 2022 12:17:58: 1000000 INFO @ Tue, 02 Aug 2022 12:18:03: 7000000 INFO @ Tue, 02 Aug 2022 12:18:05: 2000000 INFO @ Tue, 02 Aug 2022 12:18:05: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:18:05: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:18:05: #1 total tags in treatment: 3264946 INFO @ Tue, 02 Aug 2022 12:18:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:18:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:18:05: #1 tags after filtering in treatment: 2735809 INFO @ Tue, 02 Aug 2022 12:18:05: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 12:18:05: #1 finished! INFO @ Tue, 02 Aug 2022 12:18:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:18:06: #2 number of paired peaks: 1243 INFO @ Tue, 02 Aug 2022 12:18:06: start model_add_line... INFO @ Tue, 02 Aug 2022 12:18:06: start X-correlation... INFO @ Tue, 02 Aug 2022 12:18:06: end of X-cor INFO @ Tue, 02 Aug 2022 12:18:06: #2 finished! INFO @ Tue, 02 Aug 2022 12:18:06: #2 predicted fragment length is 151 bps INFO @ Tue, 02 Aug 2022 12:18:06: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 02 Aug 2022 12:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.10_model.r INFO @ Tue, 02 Aug 2022 12:18:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:18:11: 3000000 INFO @ Tue, 02 Aug 2022 12:18:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:18:16: 4000000 INFO @ Tue, 02 Aug 2022 12:18:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:18:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:18:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.10_summits.bed INFO @ Tue, 02 Aug 2022 12:18:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (589 records, 4 fields): 59 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:18:22: 5000000 INFO @ Tue, 02 Aug 2022 12:18:28: 6000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:18:34: 7000000 INFO @ Tue, 02 Aug 2022 12:18:36: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 12:18:36: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 12:18:36: #1 total tags in treatment: 3264946 INFO @ Tue, 02 Aug 2022 12:18:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:18:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:18:36: #1 tags after filtering in treatment: 2735809 INFO @ Tue, 02 Aug 2022 12:18:36: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 02 Aug 2022 12:18:36: #1 finished! INFO @ Tue, 02 Aug 2022 12:18:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:18:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:18:36: #2 number of paired peaks: 1243 INFO @ Tue, 02 Aug 2022 12:18:36: start model_add_line... INFO @ Tue, 02 Aug 2022 12:18:36: start X-correlation... INFO @ Tue, 02 Aug 2022 12:18:36: end of X-cor INFO @ Tue, 02 Aug 2022 12:18:36: #2 finished! INFO @ Tue, 02 Aug 2022 12:18:36: #2 predicted fragment length is 151 bps INFO @ Tue, 02 Aug 2022 12:18:36: #2 alternative fragment length(s) may be 151 bps INFO @ Tue, 02 Aug 2022 12:18:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.20_model.r INFO @ Tue, 02 Aug 2022 12:18:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:18:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:18:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9091669/SRX9091669.20_summits.bed INFO @ Tue, 02 Aug 2022 12:18:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (296 records, 4 fields): 100 millis CompletedMACS2peakCalling