Job ID = 6457781 SRX = SRX475422 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:10:04 prefetch.2.10.7: 1) Downloading 'SRR1175612'... 2020-06-21T12:10:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:10:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:10:52 prefetch.2.10.7: 'SRR1175612' is valid 2020-06-21T12:10:52 prefetch.2.10.7: 1) 'SRR1175612' was downloaded successfully Read 4000000 spots for SRR1175612/SRR1175612.sra Written 4000000 spots for SRR1175612/SRR1175612.sra 2020-06-21T12:11:15 prefetch.2.10.7: 1) Downloading 'SRR1175613'... 2020-06-21T12:11:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:11:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:11:43 prefetch.2.10.7: 'SRR1175613' is valid 2020-06-21T12:11:43 prefetch.2.10.7: 1) 'SRR1175613' was downloaded successfully Read 4000000 spots for SRR1175613/SRR1175613.sra Written 4000000 spots for SRR1175613/SRR1175613.sra 2020-06-21T12:12:05 prefetch.2.10.7: 1) Downloading 'SRR1175614'... 2020-06-21T12:12:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:13:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:13:03 prefetch.2.10.7: 'SRR1175614' is valid 2020-06-21T12:13:03 prefetch.2.10.7: 1) 'SRR1175614' was downloaded successfully Read 4000000 spots for SRR1175614/SRR1175614.sra Written 4000000 spots for SRR1175614/SRR1175614.sra 2020-06-21T12:13:25 prefetch.2.10.7: 1) Downloading 'SRR1175615'... 2020-06-21T12:13:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:14:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:14:04 prefetch.2.10.7: 'SRR1175615' is valid 2020-06-21T12:14:04 prefetch.2.10.7: 1) 'SRR1175615' was downloaded successfully Read 4000000 spots for SRR1175615/SRR1175615.sra Written 4000000 spots for SRR1175615/SRR1175615.sra 2020-06-21T12:14:27 prefetch.2.10.7: 1) Downloading 'SRR1175616'... 2020-06-21T12:14:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:14:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:14:44 prefetch.2.10.7: 'SRR1175616' is valid 2020-06-21T12:14:44 prefetch.2.10.7: 1) 'SRR1175616' was downloaded successfully Read 500916 spots for SRR1175616/SRR1175616.sra Written 500916 spots for SRR1175616/SRR1175616.sra 2020-06-21T12:14:56 prefetch.2.10.7: 1) Downloading 'SRR1175617'... 2020-06-21T12:14:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:15:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:15:41 prefetch.2.10.7: 'SRR1175617' is valid 2020-06-21T12:15:41 prefetch.2.10.7: 1) 'SRR1175617' was downloaded successfully Read 4000000 spots for SRR1175617/SRR1175617.sra Written 4000000 spots for SRR1175617/SRR1175617.sra 2020-06-21T12:16:05 prefetch.2.10.7: 1) Downloading 'SRR1175618'... 2020-06-21T12:16:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:16:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:16:43 prefetch.2.10.7: 'SRR1175618' is valid 2020-06-21T12:16:43 prefetch.2.10.7: 1) 'SRR1175618' was downloaded successfully Read 4000000 spots for SRR1175618/SRR1175618.sra Written 4000000 spots for SRR1175618/SRR1175618.sra 2020-06-21T12:17:06 prefetch.2.10.7: 1) Downloading 'SRR1175619'... 2020-06-21T12:17:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:17:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:17:46 prefetch.2.10.7: 'SRR1175619' is valid 2020-06-21T12:17:46 prefetch.2.10.7: 1) 'SRR1175619' was downloaded successfully Read 4000000 spots for SRR1175619/SRR1175619.sra Written 4000000 spots for SRR1175619/SRR1175619.sra 2020-06-21T12:18:08 prefetch.2.10.7: 1) Downloading 'SRR1175620'... 2020-06-21T12:18:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:19:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:19:12 prefetch.2.10.7: 'SRR1175620' is valid 2020-06-21T12:19:12 prefetch.2.10.7: 1) 'SRR1175620' was downloaded successfully Read 4000000 spots for SRR1175620/SRR1175620.sra Written 4000000 spots for SRR1175620/SRR1175620.sra 2020-06-21T12:19:35 prefetch.2.10.7: 1) Downloading 'SRR1175621'... 2020-06-21T12:19:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:29 prefetch.2.10.7: 'SRR1175621' is valid 2020-06-21T12:20:29 prefetch.2.10.7: 1) 'SRR1175621' was downloaded successfully Read 4000000 spots for SRR1175621/SRR1175621.sra Written 4000000 spots for SRR1175621/SRR1175621.sra 2020-06-21T12:20:51 prefetch.2.10.7: 1) Downloading 'SRR1175622'... 2020-06-21T12:20:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:21:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:21:29 prefetch.2.10.7: 'SRR1175622' is valid 2020-06-21T12:21:29 prefetch.2.10.7: 1) 'SRR1175622' was downloaded successfully Read 4000000 spots for SRR1175622/SRR1175622.sra Written 4000000 spots for SRR1175622/SRR1175622.sra 2020-06-21T12:21:51 prefetch.2.10.7: 1) Downloading 'SRR1175623'... 2020-06-21T12:21:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:22:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:22:25 prefetch.2.10.7: 'SRR1175623' is valid 2020-06-21T12:22:25 prefetch.2.10.7: 1) 'SRR1175623' was downloaded successfully Read 4000000 spots for SRR1175623/SRR1175623.sra Written 4000000 spots for SRR1175623/SRR1175623.sra 2020-06-21T12:22:47 prefetch.2.10.7: 1) Downloading 'SRR1175624'... 2020-06-21T12:22:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:23:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:23:35 prefetch.2.10.7: 'SRR1175624' is valid 2020-06-21T12:23:35 prefetch.2.10.7: 1) 'SRR1175624' was downloaded successfully Read 4000000 spots for SRR1175624/SRR1175624.sra Written 4000000 spots for SRR1175624/SRR1175624.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: 00:10:44 48500916 reads; of these: 48500916 (100.00%) were unpaired; of these: 18507041 (38.16%) aligned 0 times 20183585 (41.61%) aligned exactly 1 time 9810290 (20.23%) aligned >1 times 61.84% overall alignment rate Time searching: 00:10:44 Overall time: 00:10:44 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 16 files... [bam_rmdupse_core] 21846619 / 29993875 = 0.7284 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 21:42:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.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 21:42:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:14: 1000000 INFO @ Sun, 21 Jun 2020 21:42:19: 2000000 INFO @ Sun, 21 Jun 2020 21:42:24: 3000000 INFO @ Sun, 21 Jun 2020 21:42:29: 4000000 INFO @ Sun, 21 Jun 2020 21:42:35: 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 21:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.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 21:42:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:40: 6000000 INFO @ Sun, 21 Jun 2020 21:42:44: 1000000 INFO @ Sun, 21 Jun 2020 21:42:46: 7000000 INFO @ Sun, 21 Jun 2020 21:42:50: 2000000 INFO @ Sun, 21 Jun 2020 21:42:52: 8000000 INFO @ Sun, 21 Jun 2020 21:42:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:42:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:42:52: #1 total tags in treatment: 8147256 INFO @ Sun, 21 Jun 2020 21:42:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:52: #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 21:42:53: #1 tags after filtering in treatment: 8147165 INFO @ Sun, 21 Jun 2020 21:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:53: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:54: #2 number of paired peaks: 3979 INFO @ Sun, 21 Jun 2020 21:42:54: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:54: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:54: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:54: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:54: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:42:54: #2 alternative fragment length(s) may be 3,84 bps INFO @ Sun, 21 Jun 2020 21:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.05_model.r WARNING @ Sun, 21 Jun 2020 21:42:54: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:42:54: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Sun, 21 Jun 2020 21:42:54: #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 21:42:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:55: 3000000 INFO @ Sun, 21 Jun 2020 21:43:01: 4000000 INFO @ Sun, 21 Jun 2020 21:43:06: 5000000 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 21:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.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 21:43:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:43:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:43:12: 6000000 INFO @ Sun, 21 Jun 2020 21:43:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:14: 1000000 INFO @ Sun, 21 Jun 2020 21:43:18: 7000000 INFO @ Sun, 21 Jun 2020 21:43:20: 2000000 INFO @ Sun, 21 Jun 2020 21:43:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.05_summits.bed INFO @ Sun, 21 Jun 2020 21:43:22: Done! pass1 - making usageList (681 chroms): 2 millis pass2 - checking and writing primary data (5936 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:43:23: 8000000 INFO @ Sun, 21 Jun 2020 21:43:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:43:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:43:24: #1 total tags in treatment: 8147256 INFO @ Sun, 21 Jun 2020 21:43:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:24: #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 21:43:25: #1 tags after filtering in treatment: 8147165 INFO @ Sun, 21 Jun 2020 21:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:25: 3000000 INFO @ Sun, 21 Jun 2020 21:43:26: #2 number of paired peaks: 3979 INFO @ Sun, 21 Jun 2020 21:43:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:26: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:43:26: #2 alternative fragment length(s) may be 3,84 bps INFO @ Sun, 21 Jun 2020 21:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.10_model.r WARNING @ Sun, 21 Jun 2020 21:43:26: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:26: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Sun, 21 Jun 2020 21:43:26: #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 21:43:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:43:31: 4000000 INFO @ Sun, 21 Jun 2020 21:43:36: 5000000 INFO @ Sun, 21 Jun 2020 21:43:41: 6000000 INFO @ Sun, 21 Jun 2020 21:43:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:47: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:43:53: 8000000 INFO @ Sun, 21 Jun 2020 21:43:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:43:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:43:54: #1 total tags in treatment: 8147256 INFO @ Sun, 21 Jun 2020 21:43:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:43:54: #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 21:43:54: #1 tags after filtering in treatment: 8147165 INFO @ Sun, 21 Jun 2020 21:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:43:54: #1 finished! INFO @ Sun, 21 Jun 2020 21:43:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:43:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.10_summits.bed INFO @ Sun, 21 Jun 2020 21:43:54: Done! pass1 - making usageList (611 chroms): 2 millis pass2 - checking and writing primary data (3395 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:43:55: #2 number of paired peaks: 3979 INFO @ Sun, 21 Jun 2020 21:43:55: start model_add_line... INFO @ Sun, 21 Jun 2020 21:43:55: start X-correlation... INFO @ Sun, 21 Jun 2020 21:43:55: end of X-cor INFO @ Sun, 21 Jun 2020 21:43:55: #2 finished! INFO @ Sun, 21 Jun 2020 21:43:55: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 21:43:55: #2 alternative fragment length(s) may be 3,84 bps INFO @ Sun, 21 Jun 2020 21:43:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.20_model.r WARNING @ Sun, 21 Jun 2020 21:43:55: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:43:55: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Sun, 21 Jun 2020 21:43:55: #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 21:43:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:43:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:44:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX475422/SRX475422.20_summits.bed INFO @ Sun, 21 Jun 2020 21:44:24: Done! pass1 - making usageList (507 chroms): 1 millis pass2 - checking and writing primary data (1688 records, 4 fields): 16 millis CompletedMACS2peakCalling