Job ID = 6368678 SRX = SRX5402705 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:34 prefetch.2.10.7: 1) Downloading 'SRR8602939'... 2020-06-16T00:28:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:03 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:03 prefetch.2.10.7: 1) 'SRR8602939' was downloaded successfully Read 35957579 spots for SRR8602939/SRR8602939.sra Written 35957579 spots for SRR8602939/SRR8602939.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: 00:06:22 35957579 reads; of these: 35957579 (100.00%) were unpaired; of these: 8809902 (24.50%) aligned 0 times 22996810 (63.96%) aligned exactly 1 time 4150867 (11.54%) aligned >1 times 75.50% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 4672417 / 27147677 = 0.1721 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 09:47:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.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 09:47:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:34: 1000000 INFO @ Tue, 16 Jun 2020 09:47:41: 2000000 INFO @ Tue, 16 Jun 2020 09:47:47: 3000000 INFO @ Tue, 16 Jun 2020 09:47:54: 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 09:47:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.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 09:47:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:01: 5000000 INFO @ Tue, 16 Jun 2020 09:48:04: 1000000 INFO @ Tue, 16 Jun 2020 09:48:09: 6000000 INFO @ Tue, 16 Jun 2020 09:48:12: 2000000 INFO @ Tue, 16 Jun 2020 09:48:16: 7000000 INFO @ Tue, 16 Jun 2020 09:48:19: 3000000 INFO @ Tue, 16 Jun 2020 09:48:23: 8000000 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 09:48:27: 4000000 INFO @ Tue, 16 Jun 2020 09:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.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 09:48:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:31: 9000000 INFO @ Tue, 16 Jun 2020 09:48:34: 5000000 INFO @ Tue, 16 Jun 2020 09:48:35: 1000000 INFO @ Tue, 16 Jun 2020 09:48:39: 10000000 INFO @ Tue, 16 Jun 2020 09:48:42: 2000000 INFO @ Tue, 16 Jun 2020 09:48:42: 6000000 INFO @ Tue, 16 Jun 2020 09:48:47: 11000000 INFO @ Tue, 16 Jun 2020 09:48:49: 3000000 INFO @ Tue, 16 Jun 2020 09:48:50: 7000000 INFO @ Tue, 16 Jun 2020 09:48:55: 12000000 INFO @ Tue, 16 Jun 2020 09:48:56: 4000000 INFO @ Tue, 16 Jun 2020 09:48:58: 8000000 INFO @ Tue, 16 Jun 2020 09:49:03: 5000000 INFO @ Tue, 16 Jun 2020 09:49:03: 13000000 INFO @ Tue, 16 Jun 2020 09:49:06: 9000000 INFO @ Tue, 16 Jun 2020 09:49:10: 6000000 INFO @ Tue, 16 Jun 2020 09:49:11: 14000000 INFO @ Tue, 16 Jun 2020 09:49:14: 10000000 INFO @ Tue, 16 Jun 2020 09:49:17: 7000000 INFO @ Tue, 16 Jun 2020 09:49:19: 15000000 INFO @ Tue, 16 Jun 2020 09:49:22: 11000000 INFO @ Tue, 16 Jun 2020 09:49:24: 8000000 INFO @ Tue, 16 Jun 2020 09:49:27: 16000000 INFO @ Tue, 16 Jun 2020 09:49:30: 12000000 INFO @ Tue, 16 Jun 2020 09:49:31: 9000000 INFO @ Tue, 16 Jun 2020 09:49:34: 17000000 INFO @ Tue, 16 Jun 2020 09:49:38: 13000000 INFO @ Tue, 16 Jun 2020 09:49:38: 10000000 INFO @ Tue, 16 Jun 2020 09:49:42: 18000000 INFO @ Tue, 16 Jun 2020 09:49:45: 11000000 INFO @ Tue, 16 Jun 2020 09:49:46: 14000000 INFO @ Tue, 16 Jun 2020 09:49:50: 19000000 INFO @ Tue, 16 Jun 2020 09:49:53: 12000000 INFO @ Tue, 16 Jun 2020 09:49:53: 15000000 INFO @ Tue, 16 Jun 2020 09:49:58: 20000000 INFO @ Tue, 16 Jun 2020 09:50:00: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:01: 16000000 INFO @ Tue, 16 Jun 2020 09:50:06: 21000000 INFO @ Tue, 16 Jun 2020 09:50:07: 14000000 INFO @ Tue, 16 Jun 2020 09:50:09: 17000000 INFO @ Tue, 16 Jun 2020 09:50:14: 15000000 INFO @ Tue, 16 Jun 2020 09:50:14: 22000000 INFO @ Tue, 16 Jun 2020 09:50:17: 18000000 INFO @ Tue, 16 Jun 2020 09:50:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:18: #1 total tags in treatment: 22475260 INFO @ Tue, 16 Jun 2020 09:50:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:18: #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 09:50:18: #1 tags after filtering in treatment: 22475260 INFO @ Tue, 16 Jun 2020 09:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:19: #2 number of paired peaks: 180 WARNING @ Tue, 16 Jun 2020 09:50:19: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:50:20: #2 alternative fragment length(s) may be 1,13,34,575,598 bps INFO @ Tue, 16 Jun 2020 09:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.05_model.r WARNING @ Tue, 16 Jun 2020 09:50:20: #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 09:50:20: #2 You may need to consider one of the other alternative d(s): 1,13,34,575,598 WARNING @ Tue, 16 Jun 2020 09:50:20: #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 09:50:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:21: 16000000 INFO @ Tue, 16 Jun 2020 09:50:25: 19000000 INFO @ Tue, 16 Jun 2020 09:50:28: 17000000 INFO @ Tue, 16 Jun 2020 09:50:32: 20000000 INFO @ Tue, 16 Jun 2020 09:50:35: 18000000 INFO @ Tue, 16 Jun 2020 09:50:40: 21000000 INFO @ Tue, 16 Jun 2020 09:50:42: 19000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:48: 22000000 INFO @ Tue, 16 Jun 2020 09:50:50: 20000000 INFO @ Tue, 16 Jun 2020 09:50:51: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:51: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:51: #1 total tags in treatment: 22475260 INFO @ Tue, 16 Jun 2020 09:50:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:51: #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 09:50:52: #1 tags after filtering in treatment: 22475260 INFO @ Tue, 16 Jun 2020 09:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:53: #2 number of paired peaks: 180 WARNING @ Tue, 16 Jun 2020 09:50:53: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:53: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:50:53: #2 alternative fragment length(s) may be 1,13,34,575,598 bps INFO @ Tue, 16 Jun 2020 09:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.10_model.r WARNING @ Tue, 16 Jun 2020 09:50:53: #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 09:50:53: #2 You may need to consider one of the other alternative d(s): 1,13,34,575,598 WARNING @ Tue, 16 Jun 2020 09:50:53: #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 09:50:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:57: 21000000 INFO @ Tue, 16 Jun 2020 09:51:03: 22000000 INFO @ Tue, 16 Jun 2020 09:51:06: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:06: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:06: #1 total tags in treatment: 22475260 INFO @ Tue, 16 Jun 2020 09:51:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:07: #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 09:51:07: #1 tags after filtering in treatment: 22475260 INFO @ Tue, 16 Jun 2020 09:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:08: #2 number of paired peaks: 180 WARNING @ Tue, 16 Jun 2020 09:51:08: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:09: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:51:09: #2 alternative fragment length(s) may be 1,13,34,575,598 bps INFO @ Tue, 16 Jun 2020 09:51:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.20_model.r WARNING @ Tue, 16 Jun 2020 09:51:09: #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 09:51:09: #2 You may need to consider one of the other alternative d(s): 1,13,34,575,598 WARNING @ Tue, 16 Jun 2020 09:51:09: #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 09:51:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.10_summits.bed INFO @ Tue, 16 Jun 2020 09:51:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402705/SRX5402705.20_summits.bed INFO @ Tue, 16 Jun 2020 09:51:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling