Job ID = 6458413 SRX = SRX5226973 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:29 prefetch.2.10.7: 1) Downloading 'SRR8417888'... 2020-06-21T12:37:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:40:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:40:10 prefetch.2.10.7: 'SRR8417888' is valid 2020-06-21T12:40:10 prefetch.2.10.7: 1) 'SRR8417888' was downloaded successfully 2020-06-21T12:40:10 prefetch.2.10.7: 'SRR8417888' has 0 unresolved dependencies Read 15845425 spots for SRR8417888/SRR8417888.sra Written 15845425 spots for SRR8417888/SRR8417888.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: 00:05:35 15845425 reads; of these: 15845425 (100.00%) were unpaired; of these: 1681004 (10.61%) aligned 0 times 10366671 (65.42%) aligned exactly 1 time 3797750 (23.97%) aligned >1 times 89.39% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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] 1662072 / 14164421 = 0.1173 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 21:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.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 21:51:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:51:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:51:50: 1000000 INFO @ Sun, 21 Jun 2020 21:51:57: 2000000 INFO @ Sun, 21 Jun 2020 21:52:04: 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 21:52:12: 4000000 INFO @ Sun, 21 Jun 2020 21:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.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 21:52:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:20: 5000000 INFO @ Sun, 21 Jun 2020 21:52:22: 1000000 INFO @ Sun, 21 Jun 2020 21:52:29: 6000000 INFO @ Sun, 21 Jun 2020 21:52:31: 2000000 INFO @ Sun, 21 Jun 2020 21:52:38: 7000000 INFO @ Sun, 21 Jun 2020 21:52:40: 3000000 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 21:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.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 21:52:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:52:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:52:46: 8000000 INFO @ Sun, 21 Jun 2020 21:52:49: 4000000 INFO @ Sun, 21 Jun 2020 21:52:51: 1000000 INFO @ Sun, 21 Jun 2020 21:52:55: 9000000 INFO @ Sun, 21 Jun 2020 21:52:59: 5000000 INFO @ Sun, 21 Jun 2020 21:53:00: 2000000 INFO @ Sun, 21 Jun 2020 21:53:03: 10000000 INFO @ Sun, 21 Jun 2020 21:53:08: 6000000 INFO @ Sun, 21 Jun 2020 21:53:09: 3000000 INFO @ Sun, 21 Jun 2020 21:53:12: 11000000 INFO @ Sun, 21 Jun 2020 21:53:17: 4000000 INFO @ Sun, 21 Jun 2020 21:53:18: 7000000 INFO @ Sun, 21 Jun 2020 21:53:21: 12000000 INFO @ Sun, 21 Jun 2020 21:53:26: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:53:26: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:53:26: #1 total tags in treatment: 12502349 INFO @ Sun, 21 Jun 2020 21:53:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:53:26: #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 21:53:26: 5000000 INFO @ Sun, 21 Jun 2020 21:53:26: #1 tags after filtering in treatment: 12502187 INFO @ Sun, 21 Jun 2020 21:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:53:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:53:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:53:27: 8000000 INFO @ Sun, 21 Jun 2020 21:53:27: #2 number of paired peaks: 1165 INFO @ Sun, 21 Jun 2020 21:53:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:53:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:53:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:53:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:53:27: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:53:27: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 21:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.05_model.r WARNING @ Sun, 21 Jun 2020 21:53:27: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:53:27: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 21:53:27: #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 21:53:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:53:34: 6000000 INFO @ Sun, 21 Jun 2020 21:53:36: 9000000 INFO @ Sun, 21 Jun 2020 21:53:43: 7000000 INFO @ Sun, 21 Jun 2020 21:53:46: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:53:51: 8000000 INFO @ Sun, 21 Jun 2020 21:53:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:53:56: 11000000 INFO @ Sun, 21 Jun 2020 21:54:00: 9000000 INFO @ Sun, 21 Jun 2020 21:54:05: 12000000 INFO @ Sun, 21 Jun 2020 21:54:08: 10000000 INFO @ Sun, 21 Jun 2020 21:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.05_summits.bed INFO @ Sun, 21 Jun 2020 21:54:10: Done! INFO @ Sun, 21 Jun 2020 21:54:10: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:54:10: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:54:10: #1 total tags in treatment: 12502349 INFO @ Sun, 21 Jun 2020 21:54:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (464 chroms): 1 millis pass2 - checking and writing primary data (4230 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:54:11: #1 tags after filtering in treatment: 12502187 INFO @ Sun, 21 Jun 2020 21:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:11: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:12: #2 number of paired peaks: 1165 INFO @ Sun, 21 Jun 2020 21:54:12: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:12: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:12: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:12: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:12: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:54:12: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 21:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.10_model.r WARNING @ Sun, 21 Jun 2020 21:54:12: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:12: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 21:54:12: #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 21:54:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:54:16: 11000000 INFO @ Sun, 21 Jun 2020 21:54:22: 12000000 INFO @ Sun, 21 Jun 2020 21:54:26: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:54:26: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:54:26: #1 total tags in treatment: 12502349 INFO @ Sun, 21 Jun 2020 21:54:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:26: #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 21:54:26: #1 tags after filtering in treatment: 12502187 INFO @ Sun, 21 Jun 2020 21:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:26: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:27: #2 number of paired peaks: 1165 INFO @ Sun, 21 Jun 2020 21:54:27: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:27: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:27: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:27: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:27: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:54:27: #2 alternative fragment length(s) may be 91 bps INFO @ Sun, 21 Jun 2020 21:54:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.20_model.r WARNING @ Sun, 21 Jun 2020 21:54:27: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:27: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Sun, 21 Jun 2020 21:54:27: #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 21:54:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:54:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:54:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:54:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:54:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.10_summits.bed INFO @ Sun, 21 Jun 2020 21:54:57: Done! pass1 - making usageList (349 chroms): 1 millis pass2 - checking and writing primary data (2070 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226973/SRX5226973.20_summits.bed INFO @ Sun, 21 Jun 2020 21:55:10: Done! pass1 - making usageList (222 chroms): 1 millis pass2 - checking and writing primary data (785 records, 4 fields): 9 millis CompletedMACS2peakCalling