Job ID = 6507890 SRX = SRX494975 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:17:33 prefetch.2.10.7: 1) Downloading 'SRR1198507'... 2020-06-26T13:17:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:20:10 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:20:10 prefetch.2.10.7: 1) 'SRR1198507' was downloaded successfully Read 33231749 spots for SRR1198507/SRR1198507.sra Written 33231749 spots for SRR1198507/SRR1198507.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: 00:05:59 33231749 reads; of these: 33231749 (100.00%) were unpaired; of these: 356853 (1.07%) aligned 0 times 27446784 (82.59%) aligned exactly 1 time 5428112 (16.33%) aligned >1 times 98.93% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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 12 files... [bam_rmdupse_core] 7402964 / 32874896 = 0.2252 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 22:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.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 22:33:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:33:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:34:04: 1000000 INFO @ Fri, 26 Jun 2020 22:34:10: 2000000 INFO @ Fri, 26 Jun 2020 22:34:16: 3000000 INFO @ Fri, 26 Jun 2020 22:34:22: 4000000 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 22:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.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 22:34:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:34:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:34:29: 5000000 INFO @ Fri, 26 Jun 2020 22:34:35: 1000000 INFO @ Fri, 26 Jun 2020 22:34:35: 6000000 INFO @ Fri, 26 Jun 2020 22:34:41: 2000000 INFO @ Fri, 26 Jun 2020 22:34:41: 7000000 INFO @ Fri, 26 Jun 2020 22:34:48: 8000000 INFO @ Fri, 26 Jun 2020 22:34:48: 3000000 INFO @ Fri, 26 Jun 2020 22:34:54: 9000000 INFO @ Fri, 26 Jun 2020 22:34:55: 4000000 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 22:34:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.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 22:34:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:34:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:35:01: 10000000 INFO @ Fri, 26 Jun 2020 22:35:01: 5000000 INFO @ Fri, 26 Jun 2020 22:35:04: 1000000 INFO @ Fri, 26 Jun 2020 22:35:07: 11000000 INFO @ Fri, 26 Jun 2020 22:35:08: 6000000 INFO @ Fri, 26 Jun 2020 22:35:10: 2000000 INFO @ Fri, 26 Jun 2020 22:35:14: 12000000 INFO @ Fri, 26 Jun 2020 22:35:15: 7000000 INFO @ Fri, 26 Jun 2020 22:35:16: 3000000 INFO @ Fri, 26 Jun 2020 22:35:21: 13000000 INFO @ Fri, 26 Jun 2020 22:35:22: 8000000 INFO @ Fri, 26 Jun 2020 22:35:22: 4000000 INFO @ Fri, 26 Jun 2020 22:35:27: 14000000 INFO @ Fri, 26 Jun 2020 22:35:28: 5000000 INFO @ Fri, 26 Jun 2020 22:35:28: 9000000 INFO @ Fri, 26 Jun 2020 22:35:33: 15000000 INFO @ Fri, 26 Jun 2020 22:35:34: 6000000 INFO @ Fri, 26 Jun 2020 22:35:35: 10000000 INFO @ Fri, 26 Jun 2020 22:35:40: 16000000 INFO @ Fri, 26 Jun 2020 22:35:40: 7000000 INFO @ Fri, 26 Jun 2020 22:35:42: 11000000 INFO @ Fri, 26 Jun 2020 22:35:46: 17000000 INFO @ Fri, 26 Jun 2020 22:35:46: 8000000 INFO @ Fri, 26 Jun 2020 22:35:49: 12000000 INFO @ Fri, 26 Jun 2020 22:35:52: 18000000 INFO @ Fri, 26 Jun 2020 22:35:52: 9000000 INFO @ Fri, 26 Jun 2020 22:35:55: 13000000 INFO @ Fri, 26 Jun 2020 22:35:58: 19000000 INFO @ Fri, 26 Jun 2020 22:35:58: 10000000 INFO @ Fri, 26 Jun 2020 22:36:02: 14000000 INFO @ Fri, 26 Jun 2020 22:36:04: 11000000 INFO @ Fri, 26 Jun 2020 22:36:05: 20000000 INFO @ Fri, 26 Jun 2020 22:36:08: 15000000 INFO @ Fri, 26 Jun 2020 22:36:10: 12000000 INFO @ Fri, 26 Jun 2020 22:36:11: 21000000 INFO @ Fri, 26 Jun 2020 22:36:14: 16000000 INFO @ Fri, 26 Jun 2020 22:36:16: 13000000 INFO @ Fri, 26 Jun 2020 22:36:17: 22000000 INFO @ Fri, 26 Jun 2020 22:36:20: 17000000 INFO @ Fri, 26 Jun 2020 22:36:22: 14000000 INFO @ Fri, 26 Jun 2020 22:36:23: 23000000 INFO @ Fri, 26 Jun 2020 22:36:26: 18000000 INFO @ Fri, 26 Jun 2020 22:36:28: 15000000 INFO @ Fri, 26 Jun 2020 22:36:29: 24000000 INFO @ Fri, 26 Jun 2020 22:36:33: 19000000 INFO @ Fri, 26 Jun 2020 22:36:34: 16000000 INFO @ Fri, 26 Jun 2020 22:36:36: 25000000 INFO @ Fri, 26 Jun 2020 22:36:39: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:36:39: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:36:39: #1 total tags in treatment: 25471932 INFO @ Fri, 26 Jun 2020 22:36:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:36:39: #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 22:36:39: 20000000 INFO @ Fri, 26 Jun 2020 22:36:39: #1 tags after filtering in treatment: 25471932 INFO @ Fri, 26 Jun 2020 22:36:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:36:39: #1 finished! INFO @ Fri, 26 Jun 2020 22:36:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:36:39: 17000000 INFO @ Fri, 26 Jun 2020 22:36:41: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 22:36:41: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 22:36:41: start model_add_line... INFO @ Fri, 26 Jun 2020 22:36:41: start X-correlation... INFO @ Fri, 26 Jun 2020 22:36:41: end of X-cor INFO @ Fri, 26 Jun 2020 22:36:41: #2 finished! INFO @ Fri, 26 Jun 2020 22:36:41: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:36:41: #2 alternative fragment length(s) may be 1,325,500,506,513,530,583 bps INFO @ Fri, 26 Jun 2020 22:36:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.05_model.r WARNING @ Fri, 26 Jun 2020 22:36:41: #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 22:36:41: #2 You may need to consider one of the other alternative d(s): 1,325,500,506,513,530,583 WARNING @ Fri, 26 Jun 2020 22:36:41: #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 22:36:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:36:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:36:45: 21000000 INFO @ Fri, 26 Jun 2020 22:36:45: 18000000 INFO @ Fri, 26 Jun 2020 22:36:51: 22000000 INFO @ Fri, 26 Jun 2020 22:36:51: 19000000 INFO @ Fri, 26 Jun 2020 22:36:56: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:36:57: 23000000 INFO @ Fri, 26 Jun 2020 22:37:02: 21000000 INFO @ Fri, 26 Jun 2020 22:37:03: 24000000 INFO @ Fri, 26 Jun 2020 22:37:08: 22000000 INFO @ Fri, 26 Jun 2020 22:37:09: 25000000 INFO @ Fri, 26 Jun 2020 22:37:11: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:37:11: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:37:11: #1 total tags in treatment: 25471932 INFO @ Fri, 26 Jun 2020 22:37:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:37:11: #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 22:37:12: #1 tags after filtering in treatment: 25471932 INFO @ Fri, 26 Jun 2020 22:37:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:37:12: #1 finished! INFO @ Fri, 26 Jun 2020 22:37:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:37:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:37:13: 23000000 INFO @ Fri, 26 Jun 2020 22:37:14: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 22:37:14: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 22:37:14: start model_add_line... INFO @ Fri, 26 Jun 2020 22:37:14: start X-correlation... INFO @ Fri, 26 Jun 2020 22:37:14: end of X-cor INFO @ Fri, 26 Jun 2020 22:37:14: #2 finished! INFO @ Fri, 26 Jun 2020 22:37:14: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:37:14: #2 alternative fragment length(s) may be 1,325,500,506,513,530,583 bps INFO @ Fri, 26 Jun 2020 22:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.10_model.r WARNING @ Fri, 26 Jun 2020 22:37:14: #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 22:37:14: #2 You may need to consider one of the other alternative d(s): 1,325,500,506,513,530,583 WARNING @ Fri, 26 Jun 2020 22:37:14: #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 22:37:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:37:18: 24000000 INFO @ Fri, 26 Jun 2020 22:37:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:37:23: 25000000 INFO @ Fri, 26 Jun 2020 22:37:26: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:37:26: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:37:26: #1 total tags in treatment: 25471932 INFO @ Fri, 26 Jun 2020 22:37:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:37:26: #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 22:37:26: #1 tags after filtering in treatment: 25471932 INFO @ Fri, 26 Jun 2020 22:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:37:26: #1 finished! INFO @ Fri, 26 Jun 2020 22:37:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:37:28: #2 number of paired peaks: 149 WARNING @ Fri, 26 Jun 2020 22:37:28: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Fri, 26 Jun 2020 22:37:28: start model_add_line... INFO @ Fri, 26 Jun 2020 22:37:28: start X-correlation... INFO @ Fri, 26 Jun 2020 22:37:28: end of X-cor INFO @ Fri, 26 Jun 2020 22:37:28: #2 finished! INFO @ Fri, 26 Jun 2020 22:37:28: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:37:28: #2 alternative fragment length(s) may be 1,325,500,506,513,530,583 bps INFO @ Fri, 26 Jun 2020 22:37:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.20_model.r WARNING @ Fri, 26 Jun 2020 22:37:28: #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 22:37:28: #2 You may need to consider one of the other alternative d(s): 1,325,500,506,513,530,583 WARNING @ Fri, 26 Jun 2020 22:37:28: #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 22:37:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:37:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:37:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:37:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:37:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.05_summits.bed INFO @ Fri, 26 Jun 2020 22:37:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:37:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.10_summits.bed INFO @ Fri, 26 Jun 2020 22:38:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:38:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494975/SRX494975.20_summits.bed INFO @ Fri, 26 Jun 2020 22:38:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling