Job ID = 6507803 SRX = SRX466519 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:57:26 prefetch.2.10.7: 1) Downloading 'SRR1163585'... 2020-06-26T13:57:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:59:14 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:59:14 prefetch.2.10.7: 1) 'SRR1163585' was downloaded successfully Read 30788149 spots for SRR1163585/SRR1163585.sra Written 30788149 spots for SRR1163585/SRR1163585.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: 00:05:21 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169815 (0.55%) aligned 0 times 25275347 (82.09%) aligned exactly 1 time 5342987 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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 8 files... [bam_rmdupse_core] 4712186 / 30618334 = 0.1539 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 23:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.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 23:12:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:12:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:12:47: 1000000 INFO @ Fri, 26 Jun 2020 23:12:52: 2000000 INFO @ Fri, 26 Jun 2020 23:12:57: 3000000 INFO @ Fri, 26 Jun 2020 23:13:02: 4000000 INFO @ Fri, 26 Jun 2020 23:13:07: 5000000 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 23:13:12: 6000000 INFO @ Fri, 26 Jun 2020 23:13:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.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 23:13:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:13:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:13:17: 7000000 INFO @ Fri, 26 Jun 2020 23:13:18: 1000000 INFO @ Fri, 26 Jun 2020 23:13:23: 8000000 INFO @ Fri, 26 Jun 2020 23:13:23: 2000000 INFO @ Fri, 26 Jun 2020 23:13:28: 9000000 INFO @ Fri, 26 Jun 2020 23:13:28: 3000000 INFO @ Fri, 26 Jun 2020 23:13:33: 10000000 INFO @ Fri, 26 Jun 2020 23:13:34: 4000000 INFO @ Fri, 26 Jun 2020 23:13:38: 11000000 INFO @ Fri, 26 Jun 2020 23:13:39: 5000000 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 23:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.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 23:13:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:13:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:13:44: 12000000 INFO @ Fri, 26 Jun 2020 23:13:44: 6000000 INFO @ Fri, 26 Jun 2020 23:13:48: 1000000 INFO @ Fri, 26 Jun 2020 23:13:49: 13000000 INFO @ Fri, 26 Jun 2020 23:13:50: 7000000 INFO @ Fri, 26 Jun 2020 23:13:53: 2000000 INFO @ Fri, 26 Jun 2020 23:13:55: 14000000 INFO @ Fri, 26 Jun 2020 23:13:55: 8000000 INFO @ Fri, 26 Jun 2020 23:13:59: 3000000 INFO @ Fri, 26 Jun 2020 23:14:00: 15000000 INFO @ Fri, 26 Jun 2020 23:14:00: 9000000 INFO @ Fri, 26 Jun 2020 23:14:04: 4000000 INFO @ Fri, 26 Jun 2020 23:14:05: 16000000 INFO @ Fri, 26 Jun 2020 23:14:06: 10000000 INFO @ Fri, 26 Jun 2020 23:14:09: 5000000 INFO @ Fri, 26 Jun 2020 23:14:11: 17000000 INFO @ Fri, 26 Jun 2020 23:14:11: 11000000 INFO @ Fri, 26 Jun 2020 23:14:15: 6000000 INFO @ Fri, 26 Jun 2020 23:14:16: 18000000 INFO @ Fri, 26 Jun 2020 23:14:16: 12000000 INFO @ Fri, 26 Jun 2020 23:14:20: 7000000 INFO @ Fri, 26 Jun 2020 23:14:21: 19000000 INFO @ Fri, 26 Jun 2020 23:14:22: 13000000 INFO @ Fri, 26 Jun 2020 23:14:25: 8000000 INFO @ Fri, 26 Jun 2020 23:14:26: 20000000 INFO @ Fri, 26 Jun 2020 23:14:27: 14000000 INFO @ Fri, 26 Jun 2020 23:14:31: 9000000 INFO @ Fri, 26 Jun 2020 23:14:32: 21000000 INFO @ Fri, 26 Jun 2020 23:14:32: 15000000 INFO @ Fri, 26 Jun 2020 23:14:36: 10000000 INFO @ Fri, 26 Jun 2020 23:14:37: 22000000 INFO @ Fri, 26 Jun 2020 23:14:38: 16000000 INFO @ Fri, 26 Jun 2020 23:14:41: 11000000 INFO @ Fri, 26 Jun 2020 23:14:42: 23000000 INFO @ Fri, 26 Jun 2020 23:14:43: 17000000 INFO @ Fri, 26 Jun 2020 23:14:47: 12000000 INFO @ Fri, 26 Jun 2020 23:14:47: 24000000 INFO @ Fri, 26 Jun 2020 23:14:48: 18000000 INFO @ Fri, 26 Jun 2020 23:14:52: 13000000 INFO @ Fri, 26 Jun 2020 23:14:52: 25000000 INFO @ Fri, 26 Jun 2020 23:14:54: 19000000 INFO @ Fri, 26 Jun 2020 23:14:57: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:14:57: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:14:57: #1 total tags in treatment: 25906148 INFO @ Fri, 26 Jun 2020 23:14:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:14:57: #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 23:14:57: 14000000 INFO @ Fri, 26 Jun 2020 23:14:58: #1 tags after filtering in treatment: 25906148 INFO @ Fri, 26 Jun 2020 23:14:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:14:58: #1 finished! INFO @ Fri, 26 Jun 2020 23:14:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:14:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:14:59: 20000000 INFO @ Fri, 26 Jun 2020 23:14:59: #2 number of paired peaks: 132 WARNING @ Fri, 26 Jun 2020 23:14:59: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 26 Jun 2020 23:14:59: start model_add_line... INFO @ Fri, 26 Jun 2020 23:15:00: start X-correlation... INFO @ Fri, 26 Jun 2020 23:15:00: end of X-cor INFO @ Fri, 26 Jun 2020 23:15:00: #2 finished! INFO @ Fri, 26 Jun 2020 23:15:00: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:15:00: #2 alternative fragment length(s) may be 1,12,33,251,299,414,469,534 bps INFO @ Fri, 26 Jun 2020 23:15:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.05_model.r WARNING @ Fri, 26 Jun 2020 23:15:00: #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 23:15:00: #2 You may need to consider one of the other alternative d(s): 1,12,33,251,299,414,469,534 WARNING @ Fri, 26 Jun 2020 23:15:00: #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 23:15:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:15:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:15:03: 15000000 INFO @ Fri, 26 Jun 2020 23:15:04: 21000000 INFO @ Fri, 26 Jun 2020 23:15:08: 16000000 INFO @ Fri, 26 Jun 2020 23:15:09: 22000000 INFO @ Fri, 26 Jun 2020 23:15:13: 17000000 INFO @ Fri, 26 Jun 2020 23:15:14: 23000000 INFO @ Fri, 26 Jun 2020 23:15:18: 18000000 INFO @ Fri, 26 Jun 2020 23:15:20: 24000000 INFO @ Fri, 26 Jun 2020 23:15:24: 19000000 INFO @ Fri, 26 Jun 2020 23:15:25: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:15:29: 20000000 INFO @ Fri, 26 Jun 2020 23:15:30: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:15:30: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:15:30: #1 total tags in treatment: 25906148 INFO @ Fri, 26 Jun 2020 23:15:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:15:30: #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 23:15:30: #1 tags after filtering in treatment: 25906148 INFO @ Fri, 26 Jun 2020 23:15:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:15:30: #1 finished! INFO @ Fri, 26 Jun 2020 23:15:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:15:32: #2 number of paired peaks: 132 WARNING @ Fri, 26 Jun 2020 23:15:32: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 26 Jun 2020 23:15:32: start model_add_line... INFO @ Fri, 26 Jun 2020 23:15:32: start X-correlation... INFO @ Fri, 26 Jun 2020 23:15:32: end of X-cor INFO @ Fri, 26 Jun 2020 23:15:32: #2 finished! INFO @ Fri, 26 Jun 2020 23:15:32: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:15:32: #2 alternative fragment length(s) may be 1,12,33,251,299,414,469,534 bps INFO @ Fri, 26 Jun 2020 23:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.10_model.r WARNING @ Fri, 26 Jun 2020 23:15:32: #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 23:15:32: #2 You may need to consider one of the other alternative d(s): 1,12,33,251,299,414,469,534 WARNING @ Fri, 26 Jun 2020 23:15:32: #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 23:15:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:15:34: 21000000 INFO @ Fri, 26 Jun 2020 23:15:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:15:39: 22000000 INFO @ Fri, 26 Jun 2020 23:15:44: 23000000 INFO @ Fri, 26 Jun 2020 23:15:49: 24000000 INFO @ Fri, 26 Jun 2020 23:15:53: 25000000 INFO @ Fri, 26 Jun 2020 23:15:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:15:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:15:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.05_summits.bed INFO @ Fri, 26 Jun 2020 23:15:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:15:58: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:15:58: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:15:58: #1 total tags in treatment: 25906148 INFO @ Fri, 26 Jun 2020 23:15:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:15:58: #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 23:15:58: #1 tags after filtering in treatment: 25906148 INFO @ Fri, 26 Jun 2020 23:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:15:58: #1 finished! INFO @ Fri, 26 Jun 2020 23:15:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:16:00: #2 number of paired peaks: 132 WARNING @ Fri, 26 Jun 2020 23:16:00: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 26 Jun 2020 23:16:00: start model_add_line... INFO @ Fri, 26 Jun 2020 23:16:00: start X-correlation... INFO @ Fri, 26 Jun 2020 23:16:00: end of X-cor INFO @ Fri, 26 Jun 2020 23:16:00: #2 finished! INFO @ Fri, 26 Jun 2020 23:16:00: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:16:00: #2 alternative fragment length(s) may be 1,12,33,251,299,414,469,534 bps INFO @ Fri, 26 Jun 2020 23:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.20_model.r WARNING @ Fri, 26 Jun 2020 23:16:00: #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 23:16:00: #2 You may need to consider one of the other alternative d(s): 1,12,33,251,299,414,469,534 WARNING @ Fri, 26 Jun 2020 23:16:00: #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 23:16:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:16:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:16:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:16:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:16:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:16:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.10_summits.bed INFO @ Fri, 26 Jun 2020 23:16:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:16:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:16:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:16:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:16:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466519/SRX466519.20_summits.bed INFO @ Fri, 26 Jun 2020 23:16:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling