Job ID = 6454406 SRX = SRX2035278 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:05:39 prefetch.2.10.7: 1) Downloading 'SRR4044402'... 2020-06-21T09:05:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:08:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:08:44 prefetch.2.10.7: 1) 'SRR4044402' was downloaded successfully 2020-06-21T09:08:44 prefetch.2.10.7: 'SRR4044402' has 0 unresolved dependencies Read 25625486 spots for SRR4044402/SRR4044402.sra Written 25625486 spots for SRR4044402/SRR4044402.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: 00:09:13 25625486 reads; of these: 25625486 (100.00%) were unpaired; of these: 1144139 (4.46%) aligned 0 times 19063804 (74.39%) aligned exactly 1 time 5417543 (21.14%) aligned >1 times 95.54% overall alignment rate Time searching: 00:09:13 Overall time: 00:09:13 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 12 files... [bam_rmdupse_core] 5799686 / 24481347 = 0.2369 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 18:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.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 18:25:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:23: 1000000 INFO @ Sun, 21 Jun 2020 18:25:31: 2000000 INFO @ Sun, 21 Jun 2020 18:25:39: 3000000 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 18:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.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 18:25:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:46: 4000000 INFO @ Sun, 21 Jun 2020 18:25:54: 1000000 INFO @ Sun, 21 Jun 2020 18:25:55: 5000000 INFO @ Sun, 21 Jun 2020 18:26:02: 2000000 INFO @ Sun, 21 Jun 2020 18:26:03: 6000000 INFO @ Sun, 21 Jun 2020 18:26:11: 3000000 INFO @ Sun, 21 Jun 2020 18:26:11: 7000000 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 18:26:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.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 18:26:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:19: 4000000 INFO @ Sun, 21 Jun 2020 18:26:20: 8000000 INFO @ Sun, 21 Jun 2020 18:26:23: 1000000 INFO @ Sun, 21 Jun 2020 18:26:28: 5000000 INFO @ Sun, 21 Jun 2020 18:26:28: 9000000 INFO @ Sun, 21 Jun 2020 18:26:30: 2000000 INFO @ Sun, 21 Jun 2020 18:26:36: 6000000 INFO @ Sun, 21 Jun 2020 18:26:36: 10000000 INFO @ Sun, 21 Jun 2020 18:26:38: 3000000 INFO @ Sun, 21 Jun 2020 18:26:45: 11000000 INFO @ Sun, 21 Jun 2020 18:26:45: 7000000 INFO @ Sun, 21 Jun 2020 18:26:46: 4000000 INFO @ Sun, 21 Jun 2020 18:26:53: 12000000 INFO @ Sun, 21 Jun 2020 18:26:54: 5000000 INFO @ Sun, 21 Jun 2020 18:26:54: 8000000 INFO @ Sun, 21 Jun 2020 18:27:01: 6000000 INFO @ Sun, 21 Jun 2020 18:27:02: 13000000 INFO @ Sun, 21 Jun 2020 18:27:02: 9000000 INFO @ Sun, 21 Jun 2020 18:27:09: 7000000 INFO @ Sun, 21 Jun 2020 18:27:10: 14000000 INFO @ Sun, 21 Jun 2020 18:27:11: 10000000 INFO @ Sun, 21 Jun 2020 18:27:17: 8000000 INFO @ Sun, 21 Jun 2020 18:27:19: 15000000 INFO @ Sun, 21 Jun 2020 18:27:20: 11000000 INFO @ Sun, 21 Jun 2020 18:27:25: 9000000 INFO @ Sun, 21 Jun 2020 18:27:28: 16000000 INFO @ Sun, 21 Jun 2020 18:27:29: 12000000 INFO @ Sun, 21 Jun 2020 18:27:32: 10000000 INFO @ Sun, 21 Jun 2020 18:27:36: 17000000 INFO @ Sun, 21 Jun 2020 18:27:38: 13000000 INFO @ Sun, 21 Jun 2020 18:27:40: 11000000 INFO @ Sun, 21 Jun 2020 18:27:45: 18000000 INFO @ Sun, 21 Jun 2020 18:27:47: 14000000 INFO @ Sun, 21 Jun 2020 18:27:48: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:27:51: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:27:51: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:27:51: #1 total tags in treatment: 18681661 INFO @ Sun, 21 Jun 2020 18:27:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:51: #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 18:27:51: #1 tags after filtering in treatment: 18681657 INFO @ Sun, 21 Jun 2020 18:27:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:52: #2 number of paired peaks: 1782 INFO @ Sun, 21 Jun 2020 18:27:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:53: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:53: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:53: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:53: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 18:27:53: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 18:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.05_model.r WARNING @ Sun, 21 Jun 2020 18:27:53: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:53: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sun, 21 Jun 2020 18:27:53: #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 18:27:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:55: 15000000 INFO @ Sun, 21 Jun 2020 18:27:55: 13000000 INFO @ Sun, 21 Jun 2020 18:28:03: 14000000 INFO @ Sun, 21 Jun 2020 18:28:04: 16000000 INFO @ Sun, 21 Jun 2020 18:28:11: 15000000 INFO @ Sun, 21 Jun 2020 18:28:12: 17000000 INFO @ Sun, 21 Jun 2020 18:28:19: 16000000 INFO @ Sun, 21 Jun 2020 18:28:20: 18000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:28:26: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:28:26: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:28:26: #1 total tags in treatment: 18681661 INFO @ Sun, 21 Jun 2020 18:28:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:26: #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 18:28:27: #1 tags after filtering in treatment: 18681657 INFO @ Sun, 21 Jun 2020 18:28:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:27: 17000000 INFO @ Sun, 21 Jun 2020 18:28:28: #2 number of paired peaks: 1782 INFO @ Sun, 21 Jun 2020 18:28:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:28: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:28: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:28: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:28: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 18:28:28: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 18:28:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.10_model.r WARNING @ Sun, 21 Jun 2020 18:28:28: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:28:28: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sun, 21 Jun 2020 18:28:28: #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 18:28:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:28:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:34: 18000000 INFO @ Sun, 21 Jun 2020 18:28:39: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:28:39: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:28:39: #1 total tags in treatment: 18681661 INFO @ Sun, 21 Jun 2020 18:28:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:39: #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 18:28:39: #1 tags after filtering in treatment: 18681657 INFO @ Sun, 21 Jun 2020 18:28:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:41: #2 number of paired peaks: 1782 INFO @ Sun, 21 Jun 2020 18:28:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:41: #2 predicted fragment length is 132 bps INFO @ Sun, 21 Jun 2020 18:28:41: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 21 Jun 2020 18:28:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.20_model.r WARNING @ Sun, 21 Jun 2020 18:28:41: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:28:41: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Sun, 21 Jun 2020 18:28:41: #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 18:28:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:28:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.05_summits.bed INFO @ Sun, 21 Jun 2020 18:28:51: Done! pass1 - making usageList (771 chroms): 3 millis pass2 - checking and writing primary data (15592 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:29:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:29:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.10_summits.bed INFO @ Sun, 21 Jun 2020 18:29:27: Done! pass1 - making usageList (648 chroms): 2 millis pass2 - checking and writing primary data (11615 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035278/SRX2035278.20_summits.bed INFO @ Sun, 21 Jun 2020 18:29:43: Done! pass1 - making usageList (482 chroms): 2 millis pass2 - checking and writing primary data (7729 records, 4 fields): 20 millis CompletedMACS2peakCalling