Job ID = 6497475 SRX = SRX494976 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:38:05 prefetch.2.10.7: 1) Downloading 'SRR1198508'... 2020-06-25T22:38:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:43:09 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:43:09 prefetch.2.10.7: 1) 'SRR1198508' was downloaded successfully Read 33054504 spots for SRR1198508/SRR1198508.sra Written 33054504 spots for SRR1198508/SRR1198508.sra 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 Multiseed full-index search: 00:07:18 33054504 reads; of these: 33054504 (100.00%) were unpaired; of these: 682972 (2.07%) aligned 0 times 26899378 (81.38%) aligned exactly 1 time 5472154 (16.55%) aligned >1 times 97.93% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:18 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 16 files... [bam_rmdupse_core] 10466091 / 32371532 = 0.3233 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.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 @ Fri, 26 Jun 2020 07:59:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:59:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:59:21: 1000000 INFO @ Fri, 26 Jun 2020 07:59:28: 2000000 INFO @ Fri, 26 Jun 2020 07:59:36: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:59:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.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 @ Fri, 26 Jun 2020 07:59:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:59:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:59:44: 4000000 INFO @ Fri, 26 Jun 2020 07:59:52: 1000000 INFO @ Fri, 26 Jun 2020 07:59:53: 5000000 INFO @ Fri, 26 Jun 2020 08:00:00: 2000000 INFO @ Fri, 26 Jun 2020 08:00:01: 6000000 INFO @ Fri, 26 Jun 2020 08:00:09: 3000000 INFO @ Fri, 26 Jun 2020 08:00:10: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 08:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.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 @ Fri, 26 Jun 2020 08:00:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:00:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:00:18: 4000000 INFO @ Fri, 26 Jun 2020 08:00:18: 8000000 INFO @ Fri, 26 Jun 2020 08:00:22: 1000000 INFO @ Fri, 26 Jun 2020 08:00:27: 5000000 INFO @ Fri, 26 Jun 2020 08:00:27: 9000000 INFO @ Fri, 26 Jun 2020 08:00:31: 2000000 INFO @ Fri, 26 Jun 2020 08:00:36: 10000000 INFO @ Fri, 26 Jun 2020 08:00:36: 6000000 INFO @ Fri, 26 Jun 2020 08:00:40: 3000000 INFO @ Fri, 26 Jun 2020 08:00:44: 11000000 INFO @ Fri, 26 Jun 2020 08:00:45: 7000000 INFO @ Fri, 26 Jun 2020 08:00:49: 4000000 INFO @ Fri, 26 Jun 2020 08:00:54: 12000000 INFO @ Fri, 26 Jun 2020 08:00:55: 8000000 INFO @ Fri, 26 Jun 2020 08:00:59: 5000000 INFO @ Fri, 26 Jun 2020 08:01:03: 13000000 INFO @ Fri, 26 Jun 2020 08:01:05: 9000000 INFO @ Fri, 26 Jun 2020 08:01:09: 6000000 INFO @ Fri, 26 Jun 2020 08:01:13: 14000000 INFO @ Fri, 26 Jun 2020 08:01:14: 10000000 INFO @ Fri, 26 Jun 2020 08:01:19: 7000000 INFO @ Fri, 26 Jun 2020 08:01:23: 15000000 INFO @ Fri, 26 Jun 2020 08:01:24: 11000000 INFO @ Fri, 26 Jun 2020 08:01:29: 8000000 INFO @ Fri, 26 Jun 2020 08:01:34: 16000000 INFO @ Fri, 26 Jun 2020 08:01:35: 12000000 INFO @ Fri, 26 Jun 2020 08:01:39: 9000000 INFO @ Fri, 26 Jun 2020 08:01:44: 17000000 INFO @ Fri, 26 Jun 2020 08:01:46: 13000000 INFO @ Fri, 26 Jun 2020 08:01:50: 10000000 INFO @ Fri, 26 Jun 2020 08:01:54: 18000000 INFO @ Fri, 26 Jun 2020 08:01:56: 14000000 INFO @ Fri, 26 Jun 2020 08:02:00: 11000000 INFO @ Fri, 26 Jun 2020 08:02:05: 19000000 INFO @ Fri, 26 Jun 2020 08:02:06: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:02:10: 12000000 INFO @ Fri, 26 Jun 2020 08:02:13: 20000000 INFO @ Fri, 26 Jun 2020 08:02:14: 16000000 INFO @ Fri, 26 Jun 2020 08:02:18: 13000000 INFO @ Fri, 26 Jun 2020 08:02:22: 21000000 INFO @ Fri, 26 Jun 2020 08:02:22: 17000000 INFO @ Fri, 26 Jun 2020 08:02:26: 14000000 INFO @ Fri, 26 Jun 2020 08:02:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:02:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:02:29: #1 total tags in treatment: 21905441 INFO @ Fri, 26 Jun 2020 08:02:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:02:30: #1 tags after filtering in treatment: 21905441 INFO @ Fri, 26 Jun 2020 08:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:02:30: #1 finished! INFO @ Fri, 26 Jun 2020 08:02:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:02:31: 18000000 INFO @ Fri, 26 Jun 2020 08:02:31: #2 number of paired peaks: 158 WARNING @ Fri, 26 Jun 2020 08:02:31: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 26 Jun 2020 08:02:31: start model_add_line... INFO @ Fri, 26 Jun 2020 08:02:31: start X-correlation... INFO @ Fri, 26 Jun 2020 08:02:31: end of X-cor INFO @ Fri, 26 Jun 2020 08:02:31: #2 finished! INFO @ Fri, 26 Jun 2020 08:02:31: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:02:31: #2 alternative fragment length(s) may be 1,10,46,394,564,591 bps INFO @ Fri, 26 Jun 2020 08:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.05_model.r WARNING @ Fri, 26 Jun 2020 08:02:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:02:31: #2 You may need to consider one of the other alternative d(s): 1,10,46,394,564,591 WARNING @ Fri, 26 Jun 2020 08:02:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:02:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:02:34: 15000000 INFO @ Fri, 26 Jun 2020 08:02:39: 19000000 INFO @ Fri, 26 Jun 2020 08:02:42: 16000000 INFO @ Fri, 26 Jun 2020 08:02:47: 20000000 INFO @ Fri, 26 Jun 2020 08:02:50: 17000000 INFO @ Fri, 26 Jun 2020 08:02:55: 21000000 INFO @ Fri, 26 Jun 2020 08:02:58: 18000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:03:02: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:03:02: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:03:02: #1 total tags in treatment: 21905441 INFO @ Fri, 26 Jun 2020 08:03:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:03:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:03:03: #1 tags after filtering in treatment: 21905441 INFO @ Fri, 26 Jun 2020 08:03:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:03:03: #1 finished! INFO @ Fri, 26 Jun 2020 08:03:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:03:04: #2 number of paired peaks: 158 WARNING @ Fri, 26 Jun 2020 08:03:04: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 26 Jun 2020 08:03:04: start model_add_line... INFO @ Fri, 26 Jun 2020 08:03:04: start X-correlation... INFO @ Fri, 26 Jun 2020 08:03:04: end of X-cor INFO @ Fri, 26 Jun 2020 08:03:04: #2 finished! INFO @ Fri, 26 Jun 2020 08:03:04: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:03:04: #2 alternative fragment length(s) may be 1,10,46,394,564,591 bps INFO @ Fri, 26 Jun 2020 08:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.10_model.r WARNING @ Fri, 26 Jun 2020 08:03:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:03:04: #2 You may need to consider one of the other alternative d(s): 1,10,46,394,564,591 WARNING @ Fri, 26 Jun 2020 08:03:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:03:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:03:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:03:06: 19000000 INFO @ Fri, 26 Jun 2020 08:03:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:03:14: 20000000 INFO @ Fri, 26 Jun 2020 08:03:21: 21000000 INFO @ Fri, 26 Jun 2020 08:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.05_summits.bed INFO @ Fri, 26 Jun 2020 08:03:27: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:03:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:03:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:03:28: #1 total tags in treatment: 21905441 INFO @ Fri, 26 Jun 2020 08:03:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:03:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:03:28: #1 tags after filtering in treatment: 21905441 INFO @ Fri, 26 Jun 2020 08:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:03:28: #1 finished! INFO @ Fri, 26 Jun 2020 08:03:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:03:30: #2 number of paired peaks: 158 WARNING @ Fri, 26 Jun 2020 08:03:30: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 26 Jun 2020 08:03:30: start model_add_line... INFO @ Fri, 26 Jun 2020 08:03:30: start X-correlation... INFO @ Fri, 26 Jun 2020 08:03:30: end of X-cor INFO @ Fri, 26 Jun 2020 08:03:30: #2 finished! INFO @ Fri, 26 Jun 2020 08:03:30: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:03:30: #2 alternative fragment length(s) may be 1,10,46,394,564,591 bps INFO @ Fri, 26 Jun 2020 08:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.20_model.r WARNING @ Fri, 26 Jun 2020 08:03:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:03:30: #2 You may need to consider one of the other alternative d(s): 1,10,46,394,564,591 WARNING @ Fri, 26 Jun 2020 08:03:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:03:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:03:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:03:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:03:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:03:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.10_summits.bed INFO @ Fri, 26 Jun 2020 08:03:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:04:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:04:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:04:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:04:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494976/SRX494976.20_summits.bed INFO @ Fri, 26 Jun 2020 08:04:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling