Job ID = 6528379 SRX = SRX5436057 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:51:24 prefetch.2.10.7: 1) Downloading 'SRR8637389'... 2020-06-29T14:51:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:54:22 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:54:22 prefetch.2.10.7: 1) 'SRR8637389' was downloaded successfully Read 42102024 spots for SRR8637389/SRR8637389.sra Written 42102024 spots for SRR8637389/SRR8637389.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: 00:13:31 42102024 reads; of these: 42102024 (100.00%) were unpaired; of these: 1738809 (4.13%) aligned 0 times 28587610 (67.90%) aligned exactly 1 time 11775605 (27.97%) aligned >1 times 95.87% overall alignment rate Time searching: 00:13:31 Overall time: 00:13:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 6481523 / 40363215 = 0.1606 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, 30 Jun 2020 00:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.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 @ Tue, 30 Jun 2020 00:27:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:27:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:27:08: 1000000 INFO @ Tue, 30 Jun 2020 00:27:13: 2000000 INFO @ Tue, 30 Jun 2020 00:27:18: 3000000 INFO @ Tue, 30 Jun 2020 00:27:23: 4000000 INFO @ Tue, 30 Jun 2020 00:27:28: 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 @ Tue, 30 Jun 2020 00:27:33: 6000000 INFO @ Tue, 30 Jun 2020 00:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.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 @ Tue, 30 Jun 2020 00:27:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:27:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:27:38: 7000000 INFO @ Tue, 30 Jun 2020 00:27:39: 1000000 INFO @ Tue, 30 Jun 2020 00:27:43: 8000000 INFO @ Tue, 30 Jun 2020 00:27:45: 2000000 INFO @ Tue, 30 Jun 2020 00:27:48: 9000000 INFO @ Tue, 30 Jun 2020 00:27:50: 3000000 INFO @ Tue, 30 Jun 2020 00:27:54: 10000000 INFO @ Tue, 30 Jun 2020 00:27:55: 4000000 INFO @ Tue, 30 Jun 2020 00:27:59: 11000000 INFO @ Tue, 30 Jun 2020 00:28:01: 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, 30 Jun 2020 00:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.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 @ Tue, 30 Jun 2020 00:28:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:28:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:28:04: 12000000 INFO @ Tue, 30 Jun 2020 00:28:06: 6000000 INFO @ Tue, 30 Jun 2020 00:28:09: 1000000 INFO @ Tue, 30 Jun 2020 00:28:10: 13000000 INFO @ Tue, 30 Jun 2020 00:28:11: 7000000 INFO @ Tue, 30 Jun 2020 00:28:15: 14000000 INFO @ Tue, 30 Jun 2020 00:28:16: 2000000 INFO @ Tue, 30 Jun 2020 00:28:17: 8000000 INFO @ Tue, 30 Jun 2020 00:28:20: 15000000 INFO @ Tue, 30 Jun 2020 00:28:22: 3000000 INFO @ Tue, 30 Jun 2020 00:28:22: 9000000 INFO @ Tue, 30 Jun 2020 00:28:26: 16000000 INFO @ Tue, 30 Jun 2020 00:28:28: 10000000 INFO @ Tue, 30 Jun 2020 00:28:28: 4000000 INFO @ Tue, 30 Jun 2020 00:28:31: 17000000 INFO @ Tue, 30 Jun 2020 00:28:33: 11000000 INFO @ Tue, 30 Jun 2020 00:28:34: 5000000 INFO @ Tue, 30 Jun 2020 00:28:36: 18000000 INFO @ Tue, 30 Jun 2020 00:28:39: 12000000 INFO @ Tue, 30 Jun 2020 00:28:39: 6000000 INFO @ Tue, 30 Jun 2020 00:28:42: 19000000 INFO @ Tue, 30 Jun 2020 00:28:44: 13000000 INFO @ Tue, 30 Jun 2020 00:28:45: 7000000 INFO @ Tue, 30 Jun 2020 00:28:47: 20000000 INFO @ Tue, 30 Jun 2020 00:28:49: 14000000 INFO @ Tue, 30 Jun 2020 00:28:50: 8000000 INFO @ Tue, 30 Jun 2020 00:28:52: 21000000 INFO @ Tue, 30 Jun 2020 00:28:55: 15000000 INFO @ Tue, 30 Jun 2020 00:28:55: 9000000 INFO @ Tue, 30 Jun 2020 00:28:58: 22000000 INFO @ Tue, 30 Jun 2020 00:29:00: 16000000 INFO @ Tue, 30 Jun 2020 00:29:01: 10000000 INFO @ Tue, 30 Jun 2020 00:29:03: 23000000 INFO @ Tue, 30 Jun 2020 00:29:05: 17000000 INFO @ Tue, 30 Jun 2020 00:29:06: 11000000 INFO @ Tue, 30 Jun 2020 00:29:08: 24000000 INFO @ Tue, 30 Jun 2020 00:29:11: 18000000 INFO @ Tue, 30 Jun 2020 00:29:11: 12000000 INFO @ Tue, 30 Jun 2020 00:29:13: 25000000 INFO @ Tue, 30 Jun 2020 00:29:16: 19000000 INFO @ Tue, 30 Jun 2020 00:29:16: 13000000 INFO @ Tue, 30 Jun 2020 00:29:19: 26000000 INFO @ Tue, 30 Jun 2020 00:29:21: 20000000 INFO @ Tue, 30 Jun 2020 00:29:22: 14000000 INFO @ Tue, 30 Jun 2020 00:29:24: 27000000 INFO @ Tue, 30 Jun 2020 00:29:26: 21000000 INFO @ Tue, 30 Jun 2020 00:29:27: 15000000 INFO @ Tue, 30 Jun 2020 00:29:29: 28000000 INFO @ Tue, 30 Jun 2020 00:29:32: 22000000 INFO @ Tue, 30 Jun 2020 00:29:32: 16000000 INFO @ Tue, 30 Jun 2020 00:29:34: 29000000 INFO @ Tue, 30 Jun 2020 00:29:37: 23000000 INFO @ Tue, 30 Jun 2020 00:29:38: 17000000 INFO @ Tue, 30 Jun 2020 00:29:39: 30000000 INFO @ Tue, 30 Jun 2020 00:29:42: 24000000 INFO @ Tue, 30 Jun 2020 00:29:43: 18000000 INFO @ Tue, 30 Jun 2020 00:29:45: 31000000 INFO @ Tue, 30 Jun 2020 00:29:48: 25000000 INFO @ Tue, 30 Jun 2020 00:29:48: 19000000 INFO @ Tue, 30 Jun 2020 00:29:50: 32000000 INFO @ Tue, 30 Jun 2020 00:29:53: 26000000 INFO @ Tue, 30 Jun 2020 00:29:53: 20000000 INFO @ Tue, 30 Jun 2020 00:29:55: 33000000 INFO @ Tue, 30 Jun 2020 00:29:58: 27000000 INFO @ Tue, 30 Jun 2020 00:29:59: 21000000 INFO @ Tue, 30 Jun 2020 00:30:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:30:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:30:00: #1 total tags in treatment: 33881692 INFO @ Tue, 30 Jun 2020 00:30:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:30:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:30:01: #1 tags after filtering in treatment: 33881692 INFO @ Tue, 30 Jun 2020 00:30:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:30:01: #1 finished! INFO @ Tue, 30 Jun 2020 00:30:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:30:03: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 00:30:03: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 00:30:03: start model_add_line... INFO @ Tue, 30 Jun 2020 00:30:03: start X-correlation... INFO @ Tue, 30 Jun 2020 00:30:03: end of X-cor INFO @ Tue, 30 Jun 2020 00:30:03: #2 finished! INFO @ Tue, 30 Jun 2020 00:30:03: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:30:03: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 00:30:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.05_model.r WARNING @ Tue, 30 Jun 2020 00:30:03: #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, 30 Jun 2020 00:30:03: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 00:30:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:30:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:30:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:30:03: 28000000 INFO @ Tue, 30 Jun 2020 00:30:04: 22000000 INFO @ Tue, 30 Jun 2020 00:30:08: 29000000 INFO @ Tue, 30 Jun 2020 00:30:09: 23000000 INFO @ Tue, 30 Jun 2020 00:30:14: 30000000 INFO @ Tue, 30 Jun 2020 00:30:14: 24000000 INFO @ Tue, 30 Jun 2020 00:30:19: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:30:19: 25000000 INFO @ Tue, 30 Jun 2020 00:30:24: 32000000 INFO @ Tue, 30 Jun 2020 00:30:25: 26000000 INFO @ Tue, 30 Jun 2020 00:30:29: 33000000 INFO @ Tue, 30 Jun 2020 00:30:30: 27000000 INFO @ Tue, 30 Jun 2020 00:30:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:30:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:30:34: #1 total tags in treatment: 33881692 INFO @ Tue, 30 Jun 2020 00:30:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:30:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:30:35: #1 tags after filtering in treatment: 33881692 INFO @ Tue, 30 Jun 2020 00:30:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:30:35: #1 finished! INFO @ Tue, 30 Jun 2020 00:30:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:30:35: 28000000 INFO @ Tue, 30 Jun 2020 00:30:37: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 00:30:37: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 00:30:37: start model_add_line... INFO @ Tue, 30 Jun 2020 00:30:37: start X-correlation... INFO @ Tue, 30 Jun 2020 00:30:37: end of X-cor INFO @ Tue, 30 Jun 2020 00:30:37: #2 finished! INFO @ Tue, 30 Jun 2020 00:30:37: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:30:37: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 00:30:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.10_model.r WARNING @ Tue, 30 Jun 2020 00:30:37: #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, 30 Jun 2020 00:30:37: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 00:30:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:30:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:30:40: 29000000 INFO @ Tue, 30 Jun 2020 00:30:45: 30000000 INFO @ Tue, 30 Jun 2020 00:30:50: 31000000 INFO @ Tue, 30 Jun 2020 00:30:51: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:30:55: 32000000 INFO @ Tue, 30 Jun 2020 00:31:00: 33000000 INFO @ Tue, 30 Jun 2020 00:31:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:31:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:31:05: #1 total tags in treatment: 33881692 INFO @ Tue, 30 Jun 2020 00:31:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:31:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:31:06: #1 tags after filtering in treatment: 33881692 INFO @ Tue, 30 Jun 2020 00:31:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:31:06: #1 finished! INFO @ Tue, 30 Jun 2020 00:31:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:31:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:31:08: #2 number of paired peaks: 173 WARNING @ Tue, 30 Jun 2020 00:31:08: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 30 Jun 2020 00:31:08: start model_add_line... INFO @ Tue, 30 Jun 2020 00:31:08: start X-correlation... INFO @ Tue, 30 Jun 2020 00:31:08: end of X-cor INFO @ Tue, 30 Jun 2020 00:31:08: #2 finished! INFO @ Tue, 30 Jun 2020 00:31:08: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 00:31:08: #2 alternative fragment length(s) may be 1 bps INFO @ Tue, 30 Jun 2020 00:31:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.20_model.r WARNING @ Tue, 30 Jun 2020 00:31:08: #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, 30 Jun 2020 00:31:08: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Tue, 30 Jun 2020 00:31:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:31:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:31:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.05_summits.bed INFO @ Tue, 30 Jun 2020 00:31:14: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:31:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.10_summits.bed INFO @ Tue, 30 Jun 2020 00:31:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:31:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436057/SRX5436057.20_summits.bed INFO @ Tue, 30 Jun 2020 00:32:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling