Job ID = 6367918 SRX = SRX4194212 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:49:07 prefetch.2.10.7: 1) Downloading 'SRR7291534'... 2020-06-15T23:49:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:13 prefetch.2.10.7: 'SRR7291534' is valid 2020-06-15T23:50:13 prefetch.2.10.7: 1) 'SRR7291534' was downloaded successfully 2020-06-15T23:50:13 prefetch.2.10.7: 'SRR7291534' has 0 unresolved dependencies Read 7833373 spots for SRR7291534/SRR7291534.sra Written 7833373 spots for SRR7291534/SRR7291534.sra 2020-06-15T23:50:53 prefetch.2.10.7: 1) Downloading 'SRR7291535'... 2020-06-15T23:50:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:19 prefetch.2.10.7: 'SRR7291535' is valid 2020-06-15T23:52:19 prefetch.2.10.7: 1) 'SRR7291535' was downloaded successfully 2020-06-15T23:52:19 prefetch.2.10.7: 'SRR7291535' has 0 unresolved dependencies Read 7695953 spots for SRR7291535/SRR7291535.sra Written 7695953 spots for SRR7291535/SRR7291535.sra 2020-06-15T23:53:02 prefetch.2.10.7: 1) Downloading 'SRR7291536'... 2020-06-15T23:53:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:24 prefetch.2.10.7: 'SRR7291536' is valid 2020-06-15T23:54:24 prefetch.2.10.7: 1) 'SRR7291536' was downloaded successfully 2020-06-15T23:54:24 prefetch.2.10.7: 'SRR7291536' has 0 unresolved dependencies Read 7810811 spots for SRR7291536/SRR7291536.sra Written 7810811 spots for SRR7291536/SRR7291536.sra 2020-06-15T23:55:04 prefetch.2.10.7: 1) Downloading 'SRR7291537'... 2020-06-15T23:55:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:56:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:56:50 prefetch.2.10.7: 'SRR7291537' is valid 2020-06-15T23:56:50 prefetch.2.10.7: 1) 'SRR7291537' was downloaded successfully 2020-06-15T23:56:50 prefetch.2.10.7: 'SRR7291537' has 0 unresolved dependencies Read 7595632 spots for SRR7291537/SRR7291537.sra Written 7595632 spots for SRR7291537/SRR7291537.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: 00:11:39 30935769 reads; of these: 30935769 (100.00%) were unpaired; of these: 1386018 (4.48%) aligned 0 times 24606179 (79.54%) aligned exactly 1 time 4943572 (15.98%) aligned >1 times 95.52% overall alignment rate Time searching: 00:11:39 Overall time: 00:11:39 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] 5246682 / 29549751 = 0.1776 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 @ Tue, 16 Jun 2020 09:18:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.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, 16 Jun 2020 09:18:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:43: 1000000 INFO @ Tue, 16 Jun 2020 09:18:50: 2000000 INFO @ Tue, 16 Jun 2020 09:18:56: 3000000 INFO @ Tue, 16 Jun 2020 09:19:02: 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 @ Tue, 16 Jun 2020 09:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.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, 16 Jun 2020 09:19:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:09: 5000000 INFO @ Tue, 16 Jun 2020 09:19:12: 1000000 INFO @ Tue, 16 Jun 2020 09:19:15: 6000000 INFO @ Tue, 16 Jun 2020 09:19:17: 2000000 INFO @ Tue, 16 Jun 2020 09:19:22: 7000000 INFO @ Tue, 16 Jun 2020 09:19:22: 3000000 INFO @ Tue, 16 Jun 2020 09:19:28: 4000000 INFO @ Tue, 16 Jun 2020 09:19:28: 8000000 INFO @ Tue, 16 Jun 2020 09:19:33: 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 @ Tue, 16 Jun 2020 09:19:35: 9000000 INFO @ Tue, 16 Jun 2020 09:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.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, 16 Jun 2020 09:19:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:38: 6000000 INFO @ Tue, 16 Jun 2020 09:19:41: 10000000 INFO @ Tue, 16 Jun 2020 09:19:42: 1000000 INFO @ Tue, 16 Jun 2020 09:19:44: 7000000 INFO @ Tue, 16 Jun 2020 09:19:47: 2000000 INFO @ Tue, 16 Jun 2020 09:19:48: 11000000 INFO @ Tue, 16 Jun 2020 09:19:49: 8000000 INFO @ Tue, 16 Jun 2020 09:19:53: 3000000 INFO @ Tue, 16 Jun 2020 09:19:54: 12000000 INFO @ Tue, 16 Jun 2020 09:19:55: 9000000 INFO @ Tue, 16 Jun 2020 09:19:58: 4000000 INFO @ Tue, 16 Jun 2020 09:20:00: 10000000 INFO @ Tue, 16 Jun 2020 09:20:01: 13000000 INFO @ Tue, 16 Jun 2020 09:20:04: 5000000 INFO @ Tue, 16 Jun 2020 09:20:06: 11000000 INFO @ Tue, 16 Jun 2020 09:20:07: 14000000 INFO @ Tue, 16 Jun 2020 09:20:09: 6000000 INFO @ Tue, 16 Jun 2020 09:20:11: 12000000 INFO @ Tue, 16 Jun 2020 09:20:14: 15000000 INFO @ Tue, 16 Jun 2020 09:20:15: 7000000 INFO @ Tue, 16 Jun 2020 09:20:17: 13000000 INFO @ Tue, 16 Jun 2020 09:20:20: 16000000 INFO @ Tue, 16 Jun 2020 09:20:20: 8000000 INFO @ Tue, 16 Jun 2020 09:20:23: 14000000 INFO @ Tue, 16 Jun 2020 09:20:26: 9000000 INFO @ Tue, 16 Jun 2020 09:20:27: 17000000 INFO @ Tue, 16 Jun 2020 09:20:28: 15000000 INFO @ Tue, 16 Jun 2020 09:20:32: 10000000 INFO @ Tue, 16 Jun 2020 09:20:33: 18000000 INFO @ Tue, 16 Jun 2020 09:20:34: 16000000 INFO @ Tue, 16 Jun 2020 09:20:37: 11000000 INFO @ Tue, 16 Jun 2020 09:20:39: 17000000 INFO @ Tue, 16 Jun 2020 09:20:40: 19000000 INFO @ Tue, 16 Jun 2020 09:20:43: 12000000 INFO @ Tue, 16 Jun 2020 09:20:45: 18000000 INFO @ Tue, 16 Jun 2020 09:20:47: 20000000 INFO @ Tue, 16 Jun 2020 09:20:49: 13000000 INFO @ Tue, 16 Jun 2020 09:20:51: 19000000 INFO @ Tue, 16 Jun 2020 09:20:53: 21000000 INFO @ Tue, 16 Jun 2020 09:20:54: 14000000 INFO @ Tue, 16 Jun 2020 09:20:57: 20000000 INFO @ Tue, 16 Jun 2020 09:21:00: 22000000 INFO @ Tue, 16 Jun 2020 09:21:00: 15000000 INFO @ Tue, 16 Jun 2020 09:21:02: 21000000 INFO @ Tue, 16 Jun 2020 09:21:06: 16000000 INFO @ Tue, 16 Jun 2020 09:21:07: 23000000 INFO @ Tue, 16 Jun 2020 09:21:08: 22000000 INFO @ Tue, 16 Jun 2020 09:21:12: 17000000 INFO @ Tue, 16 Jun 2020 09:21:14: 24000000 INFO @ Tue, 16 Jun 2020 09:21:14: 23000000 INFO @ Tue, 16 Jun 2020 09:21:16: #1 tag size is determined as 67 bps INFO @ Tue, 16 Jun 2020 09:21:16: #1 tag size = 67 INFO @ Tue, 16 Jun 2020 09:21:16: #1 total tags in treatment: 24303069 INFO @ Tue, 16 Jun 2020 09:21:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:21:17: #1 tags after filtering in treatment: 24303069 INFO @ Tue, 16 Jun 2020 09:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:17: 18000000 INFO @ Tue, 16 Jun 2020 09:21:18: #2 number of paired peaks: 144 WARNING @ Tue, 16 Jun 2020 09:21:18: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:19: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:21:19: #2 alternative fragment length(s) may be 1,26,46,59 bps INFO @ Tue, 16 Jun 2020 09:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.05_model.r WARNING @ Tue, 16 Jun 2020 09:21:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:19: #2 You may need to consider one of the other alternative d(s): 1,26,46,59 WARNING @ Tue, 16 Jun 2020 09:21:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:21:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:20: 24000000 INFO @ Tue, 16 Jun 2020 09:21:22: #1 tag size is determined as 67 bps INFO @ Tue, 16 Jun 2020 09:21:22: #1 tag size = 67 INFO @ Tue, 16 Jun 2020 09:21:22: #1 total tags in treatment: 24303069 INFO @ Tue, 16 Jun 2020 09:21:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:21:22: #1 tags after filtering in treatment: 24303069 INFO @ Tue, 16 Jun 2020 09:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:23: 19000000 INFO @ Tue, 16 Jun 2020 09:21:24: #2 number of paired peaks: 144 WARNING @ Tue, 16 Jun 2020 09:21:24: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:24: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:21:24: #2 alternative fragment length(s) may be 1,26,46,59 bps INFO @ Tue, 16 Jun 2020 09:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.10_model.r WARNING @ Tue, 16 Jun 2020 09:21:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:24: #2 You may need to consider one of the other alternative d(s): 1,26,46,59 WARNING @ Tue, 16 Jun 2020 09:21:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:21:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:29: 20000000 INFO @ Tue, 16 Jun 2020 09:21:34: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:40: 22000000 INFO @ Tue, 16 Jun 2020 09:21:46: 23000000 INFO @ Tue, 16 Jun 2020 09:21:51: 24000000 INFO @ Tue, 16 Jun 2020 09:21:53: #1 tag size is determined as 67 bps INFO @ Tue, 16 Jun 2020 09:21:53: #1 tag size = 67 INFO @ Tue, 16 Jun 2020 09:21:53: #1 total tags in treatment: 24303069 INFO @ Tue, 16 Jun 2020 09:21:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:21:54: #1 tags after filtering in treatment: 24303069 INFO @ Tue, 16 Jun 2020 09:21:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:55: #2 number of paired peaks: 144 WARNING @ Tue, 16 Jun 2020 09:21:55: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:55: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:21:55: #2 alternative fragment length(s) may be 1,26,46,59 bps INFO @ Tue, 16 Jun 2020 09:21:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:55: #2 You may need to consider one of the other alternative d(s): 1,26,46,59 WARNING @ Tue, 16 Jun 2020 09:21:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:21:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.05_summits.bed INFO @ Tue, 16 Jun 2020 09:22:17: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.10_summits.bed INFO @ Tue, 16 Jun 2020 09:22:20: 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 @ Tue, 16 Jun 2020 09:22:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194212/SRX4194212.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling