Job ID = 6497446 SRX = SRX494944 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:00:41 prefetch.2.10.7: 1) Downloading 'SRR1198476'... 2020-06-25T22:00:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:03:54 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:03:54 prefetch.2.10.7: 1) 'SRR1198476' was downloaded successfully Read 32317902 spots for SRR1198476/SRR1198476.sra Written 32317902 spots for SRR1198476/SRR1198476.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: 00:07:37 32317902 reads; of these: 32317902 (100.00%) were unpaired; of these: 1920083 (5.94%) aligned 0 times 24974663 (77.28%) aligned exactly 1 time 5423156 (16.78%) aligned >1 times 94.06% overall alignment rate Time searching: 00:07:37 Overall time: 00:07:37 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] 5471687 / 30397819 = 0.1800 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 07:22:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.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 07:22:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:53: 1000000 INFO @ Fri, 26 Jun 2020 07:23:01: 2000000 INFO @ Fri, 26 Jun 2020 07:23:08: 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 07:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.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 07:23:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:23:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:23:16: 4000000 INFO @ Fri, 26 Jun 2020 07:23:24: 1000000 INFO @ Fri, 26 Jun 2020 07:23:24: 5000000 INFO @ Fri, 26 Jun 2020 07:23:33: 2000000 INFO @ Fri, 26 Jun 2020 07:23:33: 6000000 INFO @ Fri, 26 Jun 2020 07:23:41: 3000000 INFO @ Fri, 26 Jun 2020 07:23:41: 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 07:23:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.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 07:23:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:23:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:23:50: 4000000 INFO @ Fri, 26 Jun 2020 07:23:50: 8000000 INFO @ Fri, 26 Jun 2020 07:23:54: 1000000 INFO @ Fri, 26 Jun 2020 07:23:58: 9000000 INFO @ Fri, 26 Jun 2020 07:23:58: 5000000 INFO @ Fri, 26 Jun 2020 07:24:03: 2000000 INFO @ Fri, 26 Jun 2020 07:24:07: 10000000 INFO @ Fri, 26 Jun 2020 07:24:07: 6000000 INFO @ Fri, 26 Jun 2020 07:24:12: 3000000 INFO @ Fri, 26 Jun 2020 07:24:15: 11000000 INFO @ Fri, 26 Jun 2020 07:24:15: 7000000 INFO @ Fri, 26 Jun 2020 07:24:20: 4000000 INFO @ Fri, 26 Jun 2020 07:24:24: 12000000 INFO @ Fri, 26 Jun 2020 07:24:24: 8000000 INFO @ Fri, 26 Jun 2020 07:24:29: 5000000 INFO @ Fri, 26 Jun 2020 07:24:32: 13000000 INFO @ Fri, 26 Jun 2020 07:24:32: 9000000 INFO @ Fri, 26 Jun 2020 07:24:38: 6000000 INFO @ Fri, 26 Jun 2020 07:24:40: 14000000 INFO @ Fri, 26 Jun 2020 07:24:40: 10000000 INFO @ Fri, 26 Jun 2020 07:24:46: 7000000 INFO @ Fri, 26 Jun 2020 07:24:48: 15000000 INFO @ Fri, 26 Jun 2020 07:24:49: 11000000 INFO @ Fri, 26 Jun 2020 07:24:55: 8000000 INFO @ Fri, 26 Jun 2020 07:24:57: 16000000 INFO @ Fri, 26 Jun 2020 07:24:57: 12000000 INFO @ Fri, 26 Jun 2020 07:25:03: 9000000 INFO @ Fri, 26 Jun 2020 07:25:05: 17000000 INFO @ Fri, 26 Jun 2020 07:25:06: 13000000 INFO @ Fri, 26 Jun 2020 07:25:12: 10000000 INFO @ Fri, 26 Jun 2020 07:25:14: 18000000 INFO @ Fri, 26 Jun 2020 07:25:14: 14000000 INFO @ Fri, 26 Jun 2020 07:25:20: 11000000 INFO @ Fri, 26 Jun 2020 07:25:22: 19000000 INFO @ Fri, 26 Jun 2020 07:25:22: 15000000 INFO @ Fri, 26 Jun 2020 07:25:29: 12000000 INFO @ Fri, 26 Jun 2020 07:25:30: 16000000 INFO @ Fri, 26 Jun 2020 07:25:30: 20000000 INFO @ Fri, 26 Jun 2020 07:25:37: 13000000 INFO @ Fri, 26 Jun 2020 07:25:38: 17000000 INFO @ Fri, 26 Jun 2020 07:25:39: 21000000 INFO @ Fri, 26 Jun 2020 07:25:46: 14000000 INFO @ Fri, 26 Jun 2020 07:25:47: 18000000 INFO @ Fri, 26 Jun 2020 07:25:47: 22000000 INFO @ Fri, 26 Jun 2020 07:25:54: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:25:55: 19000000 INFO @ Fri, 26 Jun 2020 07:25:55: 23000000 INFO @ Fri, 26 Jun 2020 07:26:01: 16000000 INFO @ Fri, 26 Jun 2020 07:26:02: 20000000 INFO @ Fri, 26 Jun 2020 07:26:03: 24000000 INFO @ Fri, 26 Jun 2020 07:26:09: 17000000 INFO @ Fri, 26 Jun 2020 07:26:10: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:26:10: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:26:10: #1 total tags in treatment: 24926132 INFO @ Fri, 26 Jun 2020 07:26:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:26:10: #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 07:26:10: 21000000 INFO @ Fri, 26 Jun 2020 07:26:11: #1 tags after filtering in treatment: 24926132 INFO @ Fri, 26 Jun 2020 07:26:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:26:11: #1 finished! INFO @ Fri, 26 Jun 2020 07:26:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:26:12: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 07:26:12: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 07:26:12: start model_add_line... INFO @ Fri, 26 Jun 2020 07:26:12: start X-correlation... INFO @ Fri, 26 Jun 2020 07:26:12: end of X-cor INFO @ Fri, 26 Jun 2020 07:26:12: #2 finished! INFO @ Fri, 26 Jun 2020 07:26:12: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:26:12: #2 alternative fragment length(s) may be 1,28,49,566 bps INFO @ Fri, 26 Jun 2020 07:26:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.05_model.r WARNING @ Fri, 26 Jun 2020 07:26:12: #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 07:26:12: #2 You may need to consider one of the other alternative d(s): 1,28,49,566 WARNING @ Fri, 26 Jun 2020 07:26:12: #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 07:26:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:26:16: 18000000 INFO @ Fri, 26 Jun 2020 07:26:17: 22000000 INFO @ Fri, 26 Jun 2020 07:26:23: 19000000 INFO @ Fri, 26 Jun 2020 07:26:24: 23000000 INFO @ Fri, 26 Jun 2020 07:26:30: 20000000 INFO @ Fri, 26 Jun 2020 07:26:31: 24000000 INFO @ Fri, 26 Jun 2020 07:26:37: 21000000 INFO @ Fri, 26 Jun 2020 07:26:37: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:26:37: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:26:37: #1 total tags in treatment: 24926132 INFO @ Fri, 26 Jun 2020 07:26:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:26:37: #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 07:26:37: #1 tags after filtering in treatment: 24926132 INFO @ Fri, 26 Jun 2020 07:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:26:37: #1 finished! INFO @ Fri, 26 Jun 2020 07:26:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:26:39: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 07:26:39: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 07:26:39: start model_add_line... INFO @ Fri, 26 Jun 2020 07:26:39: start X-correlation... INFO @ Fri, 26 Jun 2020 07:26:39: end of X-cor INFO @ Fri, 26 Jun 2020 07:26:39: #2 finished! INFO @ Fri, 26 Jun 2020 07:26:39: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:26:39: #2 alternative fragment length(s) may be 1,28,49,566 bps INFO @ Fri, 26 Jun 2020 07:26:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.10_model.r WARNING @ Fri, 26 Jun 2020 07:26:39: #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 07:26:39: #2 You may need to consider one of the other alternative d(s): 1,28,49,566 WARNING @ Fri, 26 Jun 2020 07:26:39: #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 07:26:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:26:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:26:43: 22000000 INFO @ Fri, 26 Jun 2020 07:26:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:26:49: 23000000 INFO @ Fri, 26 Jun 2020 07:26:55: 24000000 INFO @ Fri, 26 Jun 2020 07:27:01: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:27:01: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:27:01: #1 total tags in treatment: 24926132 INFO @ Fri, 26 Jun 2020 07:27:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:27:01: #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 07:27:02: #1 tags after filtering in treatment: 24926132 INFO @ Fri, 26 Jun 2020 07:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:27:02: #1 finished! INFO @ Fri, 26 Jun 2020 07:27:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:27:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:27:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:27:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.05_summits.bed INFO @ Fri, 26 Jun 2020 07:27:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:27:03: #2 number of paired peaks: 136 WARNING @ Fri, 26 Jun 2020 07:27:03: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Fri, 26 Jun 2020 07:27:03: start model_add_line... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:27:04: start X-correlation... INFO @ Fri, 26 Jun 2020 07:27:04: end of X-cor INFO @ Fri, 26 Jun 2020 07:27:04: #2 finished! INFO @ Fri, 26 Jun 2020 07:27:04: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:27:04: #2 alternative fragment length(s) may be 1,28,49,566 bps INFO @ Fri, 26 Jun 2020 07:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.20_model.r WARNING @ Fri, 26 Jun 2020 07:27:04: #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 07:27:04: #2 You may need to consider one of the other alternative d(s): 1,28,49,566 WARNING @ Fri, 26 Jun 2020 07:27:04: #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 07:27:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:27:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:27:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:27:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:27:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.10_summits.bed INFO @ Fri, 26 Jun 2020 07:27:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:27:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:27:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:27:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494944/SRX494944.20_summits.bed INFO @ Fri, 26 Jun 2020 07:27:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling