Job ID = 6368037 SRX = SRX466500 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:51:18 prefetch.2.10.7: 1) Downloading 'SRR1163566'... 2020-06-15T23:51:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:04 prefetch.2.10.7: 1) 'SRR1163566' was downloaded successfully Read 30788149 spots for SRR1163566/SRR1163566.sra Written 30788149 spots for SRR1163566/SRR1163566.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: 00:04:54 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 169804 (0.55%) aligned 0 times 25275319 (82.09%) aligned exactly 1 time 5343026 (17.35%) aligned >1 times 99.45% overall alignment rate Time searching: 00:04:54 Overall time: 00:04:54 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] 4711053 / 30618345 = 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 @ Tue, 16 Jun 2020 09:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.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 09:08:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:39: 1000000 INFO @ Tue, 16 Jun 2020 09:08:45: 2000000 INFO @ Tue, 16 Jun 2020 09:08:50: 3000000 INFO @ Tue, 16 Jun 2020 09:08:56: 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 09:09:01: 5000000 INFO @ Tue, 16 Jun 2020 09:09:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.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 09:09:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:07: 6000000 INFO @ Tue, 16 Jun 2020 09:09:08: 1000000 INFO @ Tue, 16 Jun 2020 09:09:12: 7000000 INFO @ Tue, 16 Jun 2020 09:09:13: 2000000 INFO @ Tue, 16 Jun 2020 09:09:17: 8000000 INFO @ Tue, 16 Jun 2020 09:09:18: 3000000 INFO @ Tue, 16 Jun 2020 09:09:23: 9000000 INFO @ Tue, 16 Jun 2020 09:09:23: 4000000 INFO @ Tue, 16 Jun 2020 09:09:28: 5000000 INFO @ Tue, 16 Jun 2020 09:09:28: 10000000 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 09:09:33: 6000000 INFO @ Tue, 16 Jun 2020 09:09:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.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 09:09:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:34: 11000000 INFO @ Tue, 16 Jun 2020 09:09:38: 7000000 INFO @ Tue, 16 Jun 2020 09:09:40: 1000000 INFO @ Tue, 16 Jun 2020 09:09:40: 12000000 INFO @ Tue, 16 Jun 2020 09:09:42: 8000000 INFO @ Tue, 16 Jun 2020 09:09:46: 2000000 INFO @ Tue, 16 Jun 2020 09:09:46: 13000000 INFO @ Tue, 16 Jun 2020 09:09:47: 9000000 INFO @ Tue, 16 Jun 2020 09:09:52: 3000000 INFO @ Tue, 16 Jun 2020 09:09:52: 14000000 INFO @ Tue, 16 Jun 2020 09:09:52: 10000000 INFO @ Tue, 16 Jun 2020 09:09:57: 11000000 INFO @ Tue, 16 Jun 2020 09:09:58: 4000000 INFO @ Tue, 16 Jun 2020 09:09:58: 15000000 INFO @ Tue, 16 Jun 2020 09:10:02: 12000000 INFO @ Tue, 16 Jun 2020 09:10:04: 5000000 INFO @ Tue, 16 Jun 2020 09:10:05: 16000000 INFO @ Tue, 16 Jun 2020 09:10:07: 13000000 INFO @ Tue, 16 Jun 2020 09:10:10: 6000000 INFO @ Tue, 16 Jun 2020 09:10:11: 17000000 INFO @ Tue, 16 Jun 2020 09:10:12: 14000000 INFO @ Tue, 16 Jun 2020 09:10:17: 7000000 INFO @ Tue, 16 Jun 2020 09:10:17: 18000000 INFO @ Tue, 16 Jun 2020 09:10:17: 15000000 INFO @ Tue, 16 Jun 2020 09:10:22: 16000000 INFO @ Tue, 16 Jun 2020 09:10:23: 8000000 INFO @ Tue, 16 Jun 2020 09:10:23: 19000000 INFO @ Tue, 16 Jun 2020 09:10:27: 17000000 INFO @ Tue, 16 Jun 2020 09:10:29: 9000000 INFO @ Tue, 16 Jun 2020 09:10:29: 20000000 INFO @ Tue, 16 Jun 2020 09:10:32: 18000000 INFO @ Tue, 16 Jun 2020 09:10:35: 21000000 INFO @ Tue, 16 Jun 2020 09:10:35: 10000000 INFO @ Tue, 16 Jun 2020 09:10:37: 19000000 INFO @ Tue, 16 Jun 2020 09:10:41: 22000000 INFO @ Tue, 16 Jun 2020 09:10:42: 11000000 INFO @ Tue, 16 Jun 2020 09:10:42: 20000000 INFO @ Tue, 16 Jun 2020 09:10:47: 21000000 INFO @ Tue, 16 Jun 2020 09:10:47: 23000000 INFO @ Tue, 16 Jun 2020 09:10:48: 12000000 INFO @ Tue, 16 Jun 2020 09:10:52: 22000000 INFO @ Tue, 16 Jun 2020 09:10:54: 24000000 INFO @ Tue, 16 Jun 2020 09:10:54: 13000000 INFO @ Tue, 16 Jun 2020 09:10:57: 23000000 INFO @ Tue, 16 Jun 2020 09:11:00: 25000000 INFO @ Tue, 16 Jun 2020 09:11:00: 14000000 INFO @ Tue, 16 Jun 2020 09:11:01: 24000000 INFO @ Tue, 16 Jun 2020 09:11:05: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:11:05: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:11:05: #1 total tags in treatment: 25907292 INFO @ Tue, 16 Jun 2020 09:11:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:05: #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 09:11:06: #1 tags after filtering in treatment: 25907292 INFO @ Tue, 16 Jun 2020 09:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:06: 15000000 INFO @ Tue, 16 Jun 2020 09:11:06: 25000000 INFO @ Tue, 16 Jun 2020 09:11:07: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 09:11:07: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:08: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:11:08: #2 alternative fragment length(s) may be 1,14,28,84,286,365,463,502,566 bps INFO @ Tue, 16 Jun 2020 09:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:08: #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 09:11:08: #2 You may need to consider one of the other alternative d(s): 1,14,28,84,286,365,463,502,566 WARNING @ Tue, 16 Jun 2020 09:11:08: #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 09:11:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:11: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:11:11: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:11:11: #1 total tags in treatment: 25907292 INFO @ Tue, 16 Jun 2020 09:11:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:11: #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 09:11:11: 16000000 INFO @ Tue, 16 Jun 2020 09:11:11: #1 tags after filtering in treatment: 25907292 INFO @ Tue, 16 Jun 2020 09:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:13: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 09:11:13: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:13: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:11:13: #2 alternative fragment length(s) may be 1,14,28,84,286,365,463,502,566 bps INFO @ Tue, 16 Jun 2020 09:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.10_model.r WARNING @ Tue, 16 Jun 2020 09:11:13: #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 09:11:13: #2 You may need to consider one of the other alternative d(s): 1,14,28,84,286,365,463,502,566 WARNING @ Tue, 16 Jun 2020 09:11:13: #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 09:11:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:17: 17000000 INFO @ Tue, 16 Jun 2020 09:11:22: 18000000 INFO @ Tue, 16 Jun 2020 09:11:28: 19000000 INFO @ Tue, 16 Jun 2020 09:11:33: 20000000 INFO @ Tue, 16 Jun 2020 09:11:38: 21000000 INFO @ Tue, 16 Jun 2020 09:11:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:44: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:49: 23000000 INFO @ Tue, 16 Jun 2020 09:11:55: 24000000 INFO @ Tue, 16 Jun 2020 09:11:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:01: 25000000 INFO @ Tue, 16 Jun 2020 09:12:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:05: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:12:05: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:12:05: #1 total tags in treatment: 25907292 INFO @ Tue, 16 Jun 2020 09:12:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:05: #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 09:12:06: #1 tags after filtering in treatment: 25907292 INFO @ Tue, 16 Jun 2020 09:12:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:08: #2 number of paired peaks: 134 WARNING @ Tue, 16 Jun 2020 09:12:08: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:08: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:12:08: #2 alternative fragment length(s) may be 1,14,28,84,286,365,463,502,566 bps INFO @ Tue, 16 Jun 2020 09:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:08: #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 09:12:08: #2 You may need to consider one of the other alternative d(s): 1,14,28,84,286,365,463,502,566 WARNING @ Tue, 16 Jun 2020 09:12:08: #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 09:12:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466500/SRX466500.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling