Job ID = 6455141 SRX = SRX2788642 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:46:40 prefetch.2.10.7: 1) Downloading 'SRR5515262'... 2020-06-21T09:46:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:25 prefetch.2.10.7: 1) 'SRR5515262' was downloaded successfully 2020-06-21T10:26:25 prefetch.2.10.7: 'SRR5515262' has 0 unresolved dependencies Read 127170274 spots for SRR5515262/SRR5515262.sra Written 127170274 spots for SRR5515262/SRR5515262.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: 00:44:00 127170274 reads; of these: 127170274 (100.00%) were unpaired; of these: 3251561 (2.56%) aligned 0 times 107708408 (84.70%) aligned exactly 1 time 16210305 (12.75%) aligned >1 times 97.44% overall alignment rate Time searching: 00:44:00 Overall time: 00:44:00 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 52 files... [bam_rmdupse_core] 110070093 / 123918713 = 0.8882 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 20:53:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.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 20:53:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:53:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:54:02: 1000000 INFO @ Sun, 21 Jun 2020 20:54:08: 2000000 INFO @ Sun, 21 Jun 2020 20:54:15: 3000000 INFO @ Sun, 21 Jun 2020 20:54:21: 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 20:54:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.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 20:54:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:54:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:54:28: 5000000 INFO @ Sun, 21 Jun 2020 20:54:33: 1000000 INFO @ Sun, 21 Jun 2020 20:54:35: 6000000 INFO @ Sun, 21 Jun 2020 20:54:40: 2000000 INFO @ Sun, 21 Jun 2020 20:54:42: 7000000 INFO @ Sun, 21 Jun 2020 20:54:47: 3000000 INFO @ Sun, 21 Jun 2020 20:54:49: 8000000 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 20:54:54: 4000000 INFO @ Sun, 21 Jun 2020 20:54:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.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 20:54:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:54:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:54:56: 9000000 INFO @ Sun, 21 Jun 2020 20:55:01: 5000000 INFO @ Sun, 21 Jun 2020 20:55:03: 1000000 INFO @ Sun, 21 Jun 2020 20:55:03: 10000000 INFO @ Sun, 21 Jun 2020 20:55:08: 6000000 INFO @ Sun, 21 Jun 2020 20:55:10: 2000000 INFO @ Sun, 21 Jun 2020 20:55:10: 11000000 INFO @ Sun, 21 Jun 2020 20:55:15: 7000000 INFO @ Sun, 21 Jun 2020 20:55:17: 3000000 INFO @ Sun, 21 Jun 2020 20:55:18: 12000000 INFO @ Sun, 21 Jun 2020 20:55:23: 8000000 INFO @ Sun, 21 Jun 2020 20:55:25: 4000000 INFO @ Sun, 21 Jun 2020 20:55:25: 13000000 INFO @ Sun, 21 Jun 2020 20:55:30: 9000000 INFO @ Sun, 21 Jun 2020 20:55:31: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 20:55:31: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 20:55:31: #1 total tags in treatment: 13848620 INFO @ Sun, 21 Jun 2020 20:55:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:55:31: #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 20:55:32: #1 tags after filtering in treatment: 13848479 INFO @ Sun, 21 Jun 2020 20:55:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:55:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:55:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:55:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:55:32: 5000000 INFO @ Sun, 21 Jun 2020 20:55:33: #2 number of paired peaks: 6373 INFO @ Sun, 21 Jun 2020 20:55:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:55:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:55:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:55:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:55:33: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 20:55:33: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 20:55:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.05_model.r WARNING @ Sun, 21 Jun 2020 20:55:33: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:55:33: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 20:55:33: #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 20:55:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:55:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:55:37: 10000000 INFO @ Sun, 21 Jun 2020 20:55:39: 6000000 INFO @ Sun, 21 Jun 2020 20:55:44: 11000000 INFO @ Sun, 21 Jun 2020 20:55:46: 7000000 INFO @ Sun, 21 Jun 2020 20:55:52: 12000000 INFO @ Sun, 21 Jun 2020 20:55:53: 8000000 INFO @ Sun, 21 Jun 2020 20:55:59: 13000000 INFO @ Sun, 21 Jun 2020 20:56:00: 9000000 INFO @ Sun, 21 Jun 2020 20:56:05: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 20:56:05: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 20:56:05: #1 total tags in treatment: 13848620 INFO @ Sun, 21 Jun 2020 20:56:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:56:05: #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 20:56:06: #1 tags after filtering in treatment: 13848479 INFO @ Sun, 21 Jun 2020 20:56:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:56:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:56:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:56:06: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:56:07: 10000000 INFO @ Sun, 21 Jun 2020 20:56:07: #2 number of paired peaks: 6373 INFO @ Sun, 21 Jun 2020 20:56:07: start model_add_line... INFO @ Sun, 21 Jun 2020 20:56:07: start X-correlation... INFO @ Sun, 21 Jun 2020 20:56:07: end of X-cor INFO @ Sun, 21 Jun 2020 20:56:07: #2 finished! INFO @ Sun, 21 Jun 2020 20:56:07: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 20:56:07: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 20:56:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.10_model.r WARNING @ Sun, 21 Jun 2020 20:56:07: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:56:07: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 20:56:07: #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 20:56:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:56:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:56:14: 11000000 INFO @ Sun, 21 Jun 2020 20:56:21: 12000000 INFO @ Sun, 21 Jun 2020 20:56:27: 13000000 INFO @ Sun, 21 Jun 2020 20:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.05_summits.bed INFO @ Sun, 21 Jun 2020 20:56:28: Done! pass1 - making usageList (306 chroms): 2 millis pass2 - checking and writing primary data (11941 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:56:33: #1 tag size is determined as 93 bps INFO @ Sun, 21 Jun 2020 20:56:33: #1 tag size = 93 INFO @ Sun, 21 Jun 2020 20:56:33: #1 total tags in treatment: 13848620 INFO @ Sun, 21 Jun 2020 20:56:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:56:33: #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 20:56:33: #1 tags after filtering in treatment: 13848479 INFO @ Sun, 21 Jun 2020 20:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:56:33: #1 finished! INFO @ Sun, 21 Jun 2020 20:56:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:56:35: #2 number of paired peaks: 6373 INFO @ Sun, 21 Jun 2020 20:56:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:56:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:56:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:56:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:56:35: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 20:56:35: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 20:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.20_model.r WARNING @ Sun, 21 Jun 2020 20:56:35: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:56:35: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 20:56:35: #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 20:56:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:56:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:56:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:56:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:56:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.10_summits.bed INFO @ Sun, 21 Jun 2020 20:56:59: Done! pass1 - making usageList (246 chroms): 2 millis pass2 - checking and writing primary data (9392 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:57:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788642/SRX2788642.20_summits.bed INFO @ Sun, 21 Jun 2020 20:57:28: Done! pass1 - making usageList (181 chroms): 2 millis pass2 - checking and writing primary data (7234 records, 4 fields): 13 millis CompletedMACS2peakCalling