Job ID = 6459716 SRX = SRX751568 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:28:28 prefetch.2.10.7: 1) Downloading 'SRR1640728'... 2020-06-21T13:28:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:34:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:34:35 prefetch.2.10.7: 1) 'SRR1640728' was downloaded successfully Read 46599221 spots for SRR1640728/SRR1640728.sra Written 46599221 spots for SRR1640728/SRR1640728.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: 00:18:45 46599221 reads; of these: 46599221 (100.00%) were unpaired; of these: 1797395 (3.86%) aligned 0 times 17667517 (37.91%) aligned exactly 1 time 27134309 (58.23%) aligned >1 times 96.14% overall alignment rate Time searching: 00:18:45 Overall time: 00:18:45 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 20 files... [bam_rmdupse_core] 13468774 / 44801826 = 0.3006 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 23:06:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.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 23:06:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:06:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:06:11: 1000000 INFO @ Sun, 21 Jun 2020 23:06:17: 2000000 INFO @ Sun, 21 Jun 2020 23:06:22: 3000000 INFO @ Sun, 21 Jun 2020 23:06:27: 4000000 INFO @ Sun, 21 Jun 2020 23:06:32: 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 @ Sun, 21 Jun 2020 23:06:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.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 23:06:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:06:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:06:37: 6000000 INFO @ Sun, 21 Jun 2020 23:06:42: 1000000 INFO @ Sun, 21 Jun 2020 23:06:43: 7000000 INFO @ Sun, 21 Jun 2020 23:06:48: 2000000 INFO @ Sun, 21 Jun 2020 23:06:49: 8000000 INFO @ Sun, 21 Jun 2020 23:06:53: 3000000 INFO @ Sun, 21 Jun 2020 23:06:54: 9000000 INFO @ Sun, 21 Jun 2020 23:06:59: 4000000 INFO @ Sun, 21 Jun 2020 23:07:00: 10000000 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 23:07:05: 5000000 INFO @ Sun, 21 Jun 2020 23:07:06: 11000000 INFO @ Sun, 21 Jun 2020 23:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.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 23:07:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:07:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:07:10: 6000000 INFO @ Sun, 21 Jun 2020 23:07:11: 12000000 INFO @ Sun, 21 Jun 2020 23:07:12: 1000000 INFO @ Sun, 21 Jun 2020 23:07:16: 7000000 INFO @ Sun, 21 Jun 2020 23:07:17: 13000000 INFO @ Sun, 21 Jun 2020 23:07:18: 2000000 INFO @ Sun, 21 Jun 2020 23:07:22: 8000000 INFO @ Sun, 21 Jun 2020 23:07:22: 14000000 INFO @ Sun, 21 Jun 2020 23:07:23: 3000000 INFO @ Sun, 21 Jun 2020 23:07:27: 9000000 INFO @ Sun, 21 Jun 2020 23:07:28: 15000000 INFO @ Sun, 21 Jun 2020 23:07:29: 4000000 INFO @ Sun, 21 Jun 2020 23:07:33: 10000000 INFO @ Sun, 21 Jun 2020 23:07:34: 16000000 INFO @ Sun, 21 Jun 2020 23:07:35: 5000000 INFO @ Sun, 21 Jun 2020 23:07:38: 11000000 INFO @ Sun, 21 Jun 2020 23:07:39: 17000000 INFO @ Sun, 21 Jun 2020 23:07:40: 6000000 INFO @ Sun, 21 Jun 2020 23:07:44: 12000000 INFO @ Sun, 21 Jun 2020 23:07:45: 18000000 INFO @ Sun, 21 Jun 2020 23:07:46: 7000000 INFO @ Sun, 21 Jun 2020 23:07:50: 13000000 INFO @ Sun, 21 Jun 2020 23:07:51: 19000000 INFO @ Sun, 21 Jun 2020 23:07:51: 8000000 INFO @ Sun, 21 Jun 2020 23:07:55: 14000000 INFO @ Sun, 21 Jun 2020 23:07:56: 20000000 INFO @ Sun, 21 Jun 2020 23:07:57: 9000000 INFO @ Sun, 21 Jun 2020 23:08:01: 15000000 INFO @ Sun, 21 Jun 2020 23:08:02: 21000000 INFO @ Sun, 21 Jun 2020 23:08:03: 10000000 INFO @ Sun, 21 Jun 2020 23:08:06: 16000000 INFO @ Sun, 21 Jun 2020 23:08:08: 22000000 INFO @ Sun, 21 Jun 2020 23:08:08: 11000000 INFO @ Sun, 21 Jun 2020 23:08:12: 17000000 INFO @ Sun, 21 Jun 2020 23:08:14: 12000000 INFO @ Sun, 21 Jun 2020 23:08:14: 23000000 INFO @ Sun, 21 Jun 2020 23:08:18: 18000000 INFO @ Sun, 21 Jun 2020 23:08:19: 13000000 INFO @ Sun, 21 Jun 2020 23:08:20: 24000000 INFO @ Sun, 21 Jun 2020 23:08:23: 19000000 INFO @ Sun, 21 Jun 2020 23:08:25: 14000000 INFO @ Sun, 21 Jun 2020 23:08:25: 25000000 INFO @ Sun, 21 Jun 2020 23:08:29: 20000000 INFO @ Sun, 21 Jun 2020 23:08:30: 15000000 INFO @ Sun, 21 Jun 2020 23:08:31: 26000000 INFO @ Sun, 21 Jun 2020 23:08:35: 21000000 INFO @ Sun, 21 Jun 2020 23:08:36: 16000000 INFO @ Sun, 21 Jun 2020 23:08:37: 27000000 INFO @ Sun, 21 Jun 2020 23:08:41: 22000000 INFO @ Sun, 21 Jun 2020 23:08:42: 17000000 INFO @ Sun, 21 Jun 2020 23:08:43: 28000000 INFO @ Sun, 21 Jun 2020 23:08:48: 23000000 INFO @ Sun, 21 Jun 2020 23:08:48: 18000000 INFO @ Sun, 21 Jun 2020 23:08:50: 29000000 INFO @ Sun, 21 Jun 2020 23:08:53: 19000000 INFO @ Sun, 21 Jun 2020 23:08:54: 24000000 INFO @ Sun, 21 Jun 2020 23:08:56: 30000000 INFO @ Sun, 21 Jun 2020 23:08:59: 20000000 INFO @ Sun, 21 Jun 2020 23:09:00: 25000000 INFO @ Sun, 21 Jun 2020 23:09:02: 31000000 INFO @ Sun, 21 Jun 2020 23:09:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:09:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:09:04: #1 total tags in treatment: 31333052 INFO @ Sun, 21 Jun 2020 23:09:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:09:04: #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 23:09:05: #1 tags after filtering in treatment: 31333052 INFO @ Sun, 21 Jun 2020 23:09:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:09:05: #1 finished! INFO @ Sun, 21 Jun 2020 23:09:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:09:05: #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 23:09:05: 21000000 INFO @ Sun, 21 Jun 2020 23:09:05: 26000000 INFO @ Sun, 21 Jun 2020 23:09:07: #2 number of paired peaks: 1345 INFO @ Sun, 21 Jun 2020 23:09:07: start model_add_line... INFO @ Sun, 21 Jun 2020 23:09:07: start X-correlation... INFO @ Sun, 21 Jun 2020 23:09:07: end of X-cor INFO @ Sun, 21 Jun 2020 23:09:07: #2 finished! INFO @ Sun, 21 Jun 2020 23:09:07: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:09:07: #2 alternative fragment length(s) may be 1,32 bps INFO @ Sun, 21 Jun 2020 23:09:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.05_model.r WARNING @ Sun, 21 Jun 2020 23:09:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:09:07: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Sun, 21 Jun 2020 23:09:07: #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 23:09:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:09:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:09:11: 22000000 INFO @ Sun, 21 Jun 2020 23:09:11: 27000000 INFO @ Sun, 21 Jun 2020 23:09:17: 23000000 INFO @ Sun, 21 Jun 2020 23:09:17: 28000000 INFO @ Sun, 21 Jun 2020 23:09:23: 24000000 INFO @ Sun, 21 Jun 2020 23:09:23: 29000000 INFO @ Sun, 21 Jun 2020 23:09:29: 25000000 INFO @ Sun, 21 Jun 2020 23:09:29: 30000000 INFO @ Sun, 21 Jun 2020 23:09:34: 26000000 INFO @ Sun, 21 Jun 2020 23:09:35: 31000000 INFO @ Sun, 21 Jun 2020 23:09:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:09:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:09:37: #1 total tags in treatment: 31333052 INFO @ Sun, 21 Jun 2020 23:09:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:09:37: #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 23:09:38: #1 tags after filtering in treatment: 31333052 INFO @ Sun, 21 Jun 2020 23:09:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:09:38: #1 finished! INFO @ Sun, 21 Jun 2020 23:09:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:09:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:09:40: 27000000 INFO @ Sun, 21 Jun 2020 23:09:40: #2 number of paired peaks: 1345 INFO @ Sun, 21 Jun 2020 23:09:40: start model_add_line... INFO @ Sun, 21 Jun 2020 23:09:40: start X-correlation... INFO @ Sun, 21 Jun 2020 23:09:40: end of X-cor INFO @ Sun, 21 Jun 2020 23:09:40: #2 finished! INFO @ Sun, 21 Jun 2020 23:09:40: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:09:40: #2 alternative fragment length(s) may be 1,32 bps INFO @ Sun, 21 Jun 2020 23:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.10_model.r WARNING @ Sun, 21 Jun 2020 23:09:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:09:40: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Sun, 21 Jun 2020 23:09:40: #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 23:09:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:09:45: 28000000 INFO @ Sun, 21 Jun 2020 23:09:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:09:51: 29000000 INFO @ Sun, 21 Jun 2020 23:09:56: 30000000 INFO @ Sun, 21 Jun 2020 23:10:02: 31000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:10:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 23:10:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 23:10:04: #1 total tags in treatment: 31333052 INFO @ Sun, 21 Jun 2020 23:10:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:10:04: #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 23:10:04: #1 tags after filtering in treatment: 31333052 INFO @ Sun, 21 Jun 2020 23:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:10:04: #1 finished! INFO @ Sun, 21 Jun 2020 23:10:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:10:06: #2 number of paired peaks: 1345 INFO @ Sun, 21 Jun 2020 23:10:06: start model_add_line... INFO @ Sun, 21 Jun 2020 23:10:07: start X-correlation... INFO @ Sun, 21 Jun 2020 23:10:07: end of X-cor INFO @ Sun, 21 Jun 2020 23:10:07: #2 finished! INFO @ Sun, 21 Jun 2020 23:10:07: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:10:07: #2 alternative fragment length(s) may be 1,32 bps INFO @ Sun, 21 Jun 2020 23:10:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.20_model.r WARNING @ Sun, 21 Jun 2020 23:10:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:10:07: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Sun, 21 Jun 2020 23:10:07: #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 23:10:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:10:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:10:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:10:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:10:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.05_summits.bed INFO @ Sun, 21 Jun 2020 23:10:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:10:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:10:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:10:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:10:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.10_summits.bed INFO @ Sun, 21 Jun 2020 23:10:41: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:10:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX751568/SRX751568.20_summits.bed INFO @ Sun, 21 Jun 2020 23:11:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling