Job ID = 6458768 SRX = SRX5436042 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:41:57 prefetch.2.10.7: 1) Downloading 'SRR8637374'... 2020-06-21T12:41:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:47:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:47:48 prefetch.2.10.7: 1) 'SRR8637374' was downloaded successfully Read 36586153 spots for SRR8637374/SRR8637374.sra Written 36586153 spots for SRR8637374/SRR8637374.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: 00:10:07 36586153 reads; of these: 36586153 (100.00%) were unpaired; of these: 1593020 (4.35%) aligned 0 times 23760158 (64.94%) aligned exactly 1 time 11232975 (30.70%) aligned >1 times 95.65% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 6067420 / 34993133 = 0.1734 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 @ Sun, 21 Jun 2020 22:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:06:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:55: 1000000 INFO @ Sun, 21 Jun 2020 22:07:00: 2000000 INFO @ Sun, 21 Jun 2020 22:07:06: 3000000 INFO @ Sun, 21 Jun 2020 22:07:11: 4000000 INFO @ Sun, 21 Jun 2020 22:07:16: 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 @ Sun, 21 Jun 2020 22:07:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:07:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:21: 6000000 INFO @ Sun, 21 Jun 2020 22:07:26: 1000000 INFO @ Sun, 21 Jun 2020 22:07:27: 7000000 INFO @ Sun, 21 Jun 2020 22:07:31: 2000000 INFO @ Sun, 21 Jun 2020 22:07:32: 8000000 INFO @ Sun, 21 Jun 2020 22:07:37: 3000000 INFO @ Sun, 21 Jun 2020 22:07:38: 9000000 INFO @ Sun, 21 Jun 2020 22:07:43: 4000000 INFO @ Sun, 21 Jun 2020 22:07:43: 10000000 INFO @ Sun, 21 Jun 2020 22:07:48: 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 @ Sun, 21 Jun 2020 22:07:49: 11000000 INFO @ Sun, 21 Jun 2020 22:07:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 22:07:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:54: 6000000 INFO @ Sun, 21 Jun 2020 22:07:54: 12000000 INFO @ Sun, 21 Jun 2020 22:07:56: 1000000 INFO @ Sun, 21 Jun 2020 22:08:00: 7000000 INFO @ Sun, 21 Jun 2020 22:08:00: 13000000 INFO @ Sun, 21 Jun 2020 22:08:01: 2000000 INFO @ Sun, 21 Jun 2020 22:08:05: 8000000 INFO @ Sun, 21 Jun 2020 22:08:06: 14000000 INFO @ Sun, 21 Jun 2020 22:08:07: 3000000 INFO @ Sun, 21 Jun 2020 22:08:11: 9000000 INFO @ Sun, 21 Jun 2020 22:08:11: 15000000 INFO @ Sun, 21 Jun 2020 22:08:13: 4000000 INFO @ Sun, 21 Jun 2020 22:08:17: 10000000 INFO @ Sun, 21 Jun 2020 22:08:17: 16000000 INFO @ Sun, 21 Jun 2020 22:08:18: 5000000 INFO @ Sun, 21 Jun 2020 22:08:22: 11000000 INFO @ Sun, 21 Jun 2020 22:08:23: 17000000 INFO @ Sun, 21 Jun 2020 22:08:24: 6000000 INFO @ Sun, 21 Jun 2020 22:08:28: 12000000 INFO @ Sun, 21 Jun 2020 22:08:28: 18000000 INFO @ Sun, 21 Jun 2020 22:08:30: 7000000 INFO @ Sun, 21 Jun 2020 22:08:34: 13000000 INFO @ Sun, 21 Jun 2020 22:08:34: 19000000 INFO @ Sun, 21 Jun 2020 22:08:36: 8000000 INFO @ Sun, 21 Jun 2020 22:08:39: 14000000 INFO @ Sun, 21 Jun 2020 22:08:39: 20000000 INFO @ Sun, 21 Jun 2020 22:08:41: 9000000 INFO @ Sun, 21 Jun 2020 22:08:45: 15000000 INFO @ Sun, 21 Jun 2020 22:08:45: 21000000 INFO @ Sun, 21 Jun 2020 22:08:47: 10000000 INFO @ Sun, 21 Jun 2020 22:08:51: 22000000 INFO @ Sun, 21 Jun 2020 22:08:51: 16000000 INFO @ Sun, 21 Jun 2020 22:08:52: 11000000 INFO @ Sun, 21 Jun 2020 22:08:56: 23000000 INFO @ Sun, 21 Jun 2020 22:08:56: 17000000 INFO @ Sun, 21 Jun 2020 22:08:58: 12000000 INFO @ Sun, 21 Jun 2020 22:09:02: 24000000 INFO @ Sun, 21 Jun 2020 22:09:02: 18000000 INFO @ Sun, 21 Jun 2020 22:09:03: 13000000 INFO @ Sun, 21 Jun 2020 22:09:07: 19000000 INFO @ Sun, 21 Jun 2020 22:09:08: 25000000 INFO @ Sun, 21 Jun 2020 22:09:09: 14000000 INFO @ Sun, 21 Jun 2020 22:09:13: 20000000 INFO @ Sun, 21 Jun 2020 22:09:13: 26000000 INFO @ Sun, 21 Jun 2020 22:09:15: 15000000 INFO @ Sun, 21 Jun 2020 22:09:19: 21000000 INFO @ Sun, 21 Jun 2020 22:09:19: 27000000 INFO @ Sun, 21 Jun 2020 22:09:20: 16000000 INFO @ Sun, 21 Jun 2020 22:09:24: 22000000 INFO @ Sun, 21 Jun 2020 22:09:24: 28000000 INFO @ Sun, 21 Jun 2020 22:09:26: 17000000 INFO @ Sun, 21 Jun 2020 22:09:30: 23000000 INFO @ Sun, 21 Jun 2020 22:09:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:09:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:09:30: #1 total tags in treatment: 28925713 INFO @ Sun, 21 Jun 2020 22:09:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:09:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:09:31: #1 tags after filtering in treatment: 28925668 INFO @ Sun, 21 Jun 2020 22:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:09:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:09:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:09:32: 18000000 INFO @ Sun, 21 Jun 2020 22:09:32: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 22:09:32: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 22:09:32: start model_add_line... INFO @ Sun, 21 Jun 2020 22:09:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:09:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:09:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:09:33: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:09:33: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 21 Jun 2020 22:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.05_model.r WARNING @ Sun, 21 Jun 2020 22:09:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:09:33: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 21 Jun 2020 22:09:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:09:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:09:35: 24000000 INFO @ Sun, 21 Jun 2020 22:09:37: 19000000 INFO @ Sun, 21 Jun 2020 22:09:41: 25000000 INFO @ Sun, 21 Jun 2020 22:09:43: 20000000 INFO @ Sun, 21 Jun 2020 22:09:47: 26000000 INFO @ Sun, 21 Jun 2020 22:09:48: 21000000 INFO @ Sun, 21 Jun 2020 22:09:52: 27000000 INFO @ Sun, 21 Jun 2020 22:09:53: 22000000 INFO @ Sun, 21 Jun 2020 22:09:58: 28000000 INFO @ Sun, 21 Jun 2020 22:09:59: 23000000 INFO @ Sun, 21 Jun 2020 22:10:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:10:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:10:03: #1 total tags in treatment: 28925713 INFO @ Sun, 21 Jun 2020 22:10:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:10:04: #1 tags after filtering in treatment: 28925668 INFO @ Sun, 21 Jun 2020 22:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:04: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:04: 24000000 INFO @ Sun, 21 Jun 2020 22:10:06: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 22:10:06: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:06: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:06: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:06: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:06: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:06: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:10:06: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 21 Jun 2020 22:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.10_model.r WARNING @ Sun, 21 Jun 2020 22:10:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:10:06: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 21 Jun 2020 22:10:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:10:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:10: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:10:16: 26000000 INFO @ Sun, 21 Jun 2020 22:10:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:21: 27000000 INFO @ Sun, 21 Jun 2020 22:10:26: 28000000 INFO @ Sun, 21 Jun 2020 22:10:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:10:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:10:32: #1 total tags in treatment: 28925713 INFO @ Sun, 21 Jun 2020 22:10:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:10:32: #1 tags after filtering in treatment: 28925668 INFO @ Sun, 21 Jun 2020 22:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:34: #2 number of paired peaks: 702 WARNING @ Sun, 21 Jun 2020 22:10:34: Fewer paired peaks (702) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 702 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:35: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:35: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:35: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:10:35: #2 alternative fragment length(s) may be 1,42 bps INFO @ Sun, 21 Jun 2020 22:10:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.20_model.r WARNING @ Sun, 21 Jun 2020 22:10:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:10:35: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Sun, 21 Jun 2020 22:10:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:10:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.05_summits.bed INFO @ Sun, 21 Jun 2020 22:10:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:10:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.10_summits.bed INFO @ Sun, 21 Jun 2020 22:11:10: 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 @ Sun, 21 Jun 2020 22:11:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436042/SRX5436042.20_summits.bed INFO @ Sun, 21 Jun 2020 22:11:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling