Job ID = 6455004 SRX = SRX2618550 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:53:40 prefetch.2.10.7: 1) Downloading 'SRR5319104'... 2020-06-21T09:53:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:56:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:56:16 prefetch.2.10.7: 'SRR5319104' is valid 2020-06-21T09:56:16 prefetch.2.10.7: 1) 'SRR5319104' was downloaded successfully 2020-06-21T09:56:16 prefetch.2.10.7: 'SRR5319104' has 0 unresolved dependencies Read 18796742 spots for SRR5319104/SRR5319104.sra Written 18796742 spots for SRR5319104/SRR5319104.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: 00:04:47 18796742 reads; of these: 18796742 (100.00%) were unpaired; of these: 1895556 (10.08%) aligned 0 times 12646180 (67.28%) aligned exactly 1 time 4255006 (22.64%) aligned >1 times 89.92% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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 8 files... [bam_rmdupse_core] 1946683 / 16901186 = 0.1152 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 19:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.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 19:07:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:33: 1000000 INFO @ Sun, 21 Jun 2020 19:07:38: 2000000 INFO @ Sun, 21 Jun 2020 19:07:44: 3000000 INFO @ Sun, 21 Jun 2020 19:07:49: 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 @ Sun, 21 Jun 2020 19:07:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.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 19:07:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:07:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:07:55: 5000000 INFO @ Sun, 21 Jun 2020 19:08:02: 6000000 INFO @ Sun, 21 Jun 2020 19:08:02: 1000000 INFO @ Sun, 21 Jun 2020 19:08:08: 7000000 INFO @ Sun, 21 Jun 2020 19:08:09: 2000000 INFO @ Sun, 21 Jun 2020 19:08:15: 8000000 INFO @ Sun, 21 Jun 2020 19:08:16: 3000000 INFO @ Sun, 21 Jun 2020 19:08:21: 9000000 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 19:08:23: 4000000 INFO @ Sun, 21 Jun 2020 19:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.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 19:08:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:28: 10000000 INFO @ Sun, 21 Jun 2020 19:08:31: 5000000 INFO @ Sun, 21 Jun 2020 19:08:32: 1000000 INFO @ Sun, 21 Jun 2020 19:08:34: 11000000 INFO @ Sun, 21 Jun 2020 19:08:38: 6000000 INFO @ Sun, 21 Jun 2020 19:08:38: 2000000 INFO @ Sun, 21 Jun 2020 19:08:41: 12000000 INFO @ Sun, 21 Jun 2020 19:08:45: 3000000 INFO @ Sun, 21 Jun 2020 19:08:45: 7000000 INFO @ Sun, 21 Jun 2020 19:08:48: 13000000 INFO @ Sun, 21 Jun 2020 19:08:51: 4000000 INFO @ Sun, 21 Jun 2020 19:08:52: 8000000 INFO @ Sun, 21 Jun 2020 19:08:55: 14000000 INFO @ Sun, 21 Jun 2020 19:08:58: 5000000 INFO @ Sun, 21 Jun 2020 19:08:59: 9000000 INFO @ Sun, 21 Jun 2020 19:09:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:01: #1 total tags in treatment: 14954503 INFO @ Sun, 21 Jun 2020 19:09:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:01: #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 19:09:02: #1 tags after filtering in treatment: 14954503 INFO @ Sun, 21 Jun 2020 19:09:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:03: #2 number of paired peaks: 1171 INFO @ Sun, 21 Jun 2020 19:09:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:03: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 19:09:03: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 19:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.05_model.r WARNING @ Sun, 21 Jun 2020 19:09:03: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:03: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 21 Jun 2020 19:09:03: #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 19:09:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:05: 6000000 INFO @ Sun, 21 Jun 2020 19:09:06: 10000000 INFO @ Sun, 21 Jun 2020 19:09:11: 7000000 INFO @ Sun, 21 Jun 2020 19:09:13: 11000000 INFO @ Sun, 21 Jun 2020 19:09:18: 8000000 INFO @ Sun, 21 Jun 2020 19:09:21: 12000000 INFO @ Sun, 21 Jun 2020 19:09:25: 9000000 INFO @ Sun, 21 Jun 2020 19:09:28: 13000000 INFO @ Sun, 21 Jun 2020 19:09:31: 10000000 INFO @ Sun, 21 Jun 2020 19:09:35: 14000000 INFO @ Sun, 21 Jun 2020 19:09:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:09:38: 11000000 INFO @ Sun, 21 Jun 2020 19:09:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:09:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:09:43: #1 total tags in treatment: 14954503 INFO @ Sun, 21 Jun 2020 19:09:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:09:43: #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 19:09:43: #1 tags after filtering in treatment: 14954503 INFO @ Sun, 21 Jun 2020 19:09:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:09:43: #1 finished! INFO @ Sun, 21 Jun 2020 19:09:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:09:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:09:44: #2 number of paired peaks: 1171 INFO @ Sun, 21 Jun 2020 19:09:44: start model_add_line... INFO @ Sun, 21 Jun 2020 19:09:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:09:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:09:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:09:45: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 19:09:45: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 19:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.10_model.r WARNING @ Sun, 21 Jun 2020 19:09:45: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:09:45: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 21 Jun 2020 19:09:45: #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 19:09:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:09:45: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:09:51: 13000000 INFO @ Sun, 21 Jun 2020 19:09:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:09:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:09:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.05_summits.bed INFO @ Sun, 21 Jun 2020 19:09:53: Done! pass1 - making usageList (631 chroms): 2 millis pass2 - checking and writing primary data (6775 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:09:57: 14000000 INFO @ Sun, 21 Jun 2020 19:10:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:10:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:10:03: #1 total tags in treatment: 14954503 INFO @ Sun, 21 Jun 2020 19:10:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:03: #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 19:10:03: #1 tags after filtering in treatment: 14954503 INFO @ Sun, 21 Jun 2020 19:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:04: #2 number of paired peaks: 1171 INFO @ Sun, 21 Jun 2020 19:10:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:05: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 19:10:05: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 19:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.20_model.r WARNING @ Sun, 21 Jun 2020 19:10:05: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:05: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 21 Jun 2020 19:10:05: #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 19:10:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:10:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.10_summits.bed INFO @ Sun, 21 Jun 2020 19:10:33: Done! pass1 - making usageList (529 chroms): 2 millis pass2 - checking and writing primary data (4424 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:10:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:10:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618550/SRX2618550.20_summits.bed INFO @ Sun, 21 Jun 2020 19:10:54: Done! pass1 - making usageList (425 chroms): 1 millis pass2 - checking and writing primary data (2273 records, 4 fields): 14 millis CompletedMACS2peakCalling