Job ID = 6457954 SRX = SRX4923197 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:19:07 prefetch.2.10.7: 1) Downloading 'SRR8096347'... 2020-06-21T12:19:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:25:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:25:22 prefetch.2.10.7: 1) 'SRR8096347' was downloaded successfully 2020-06-21T12:25:22 prefetch.2.10.7: 'SRR8096347' has 0 unresolved dependencies Read 76168129 spots for SRR8096347/SRR8096347.sra Written 76168129 spots for SRR8096347/SRR8096347.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: 00:00:01 Multiseed full-index search: 00:26:19 76168129 reads; of these: 76168129 (100.00%) were unpaired; of these: 1859026 (2.44%) aligned 0 times 25524369 (33.51%) aligned exactly 1 time 48784734 (64.05%) aligned >1 times 97.56% overall alignment rate Time searching: 00:26:20 Overall time: 00:26:20 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 32 files... [bam_rmdupse_core] 37746744 / 74309103 = 0.5080 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 22:06:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.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 22:06:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:21: 1000000 INFO @ Sun, 21 Jun 2020 22:06:27: 2000000 INFO @ Sun, 21 Jun 2020 22:06:32: 3000000 INFO @ Sun, 21 Jun 2020 22:06:38: 4000000 INFO @ Sun, 21 Jun 2020 22:06:43: 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 22:06:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.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 22:06:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:06:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:06:49: 6000000 INFO @ Sun, 21 Jun 2020 22:06:52: 1000000 INFO @ Sun, 21 Jun 2020 22:06:55: 7000000 INFO @ Sun, 21 Jun 2020 22:06:58: 2000000 INFO @ Sun, 21 Jun 2020 22:07:01: 8000000 INFO @ Sun, 21 Jun 2020 22:07:05: 3000000 INFO @ Sun, 21 Jun 2020 22:07:07: 9000000 INFO @ Sun, 21 Jun 2020 22:07:11: 4000000 INFO @ Sun, 21 Jun 2020 22:07:13: 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 22:07:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.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 22:07:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:07:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:07:17: 5000000 INFO @ Sun, 21 Jun 2020 22:07:19: 11000000 INFO @ Sun, 21 Jun 2020 22:07:22: 1000000 INFO @ Sun, 21 Jun 2020 22:07:23: 6000000 INFO @ Sun, 21 Jun 2020 22:07:25: 12000000 INFO @ Sun, 21 Jun 2020 22:07:28: 2000000 INFO @ Sun, 21 Jun 2020 22:07:29: 7000000 INFO @ Sun, 21 Jun 2020 22:07:32: 13000000 INFO @ Sun, 21 Jun 2020 22:07:35: 3000000 INFO @ Sun, 21 Jun 2020 22:07:35: 8000000 INFO @ Sun, 21 Jun 2020 22:07:38: 14000000 INFO @ Sun, 21 Jun 2020 22:07:41: 4000000 INFO @ Sun, 21 Jun 2020 22:07:42: 9000000 INFO @ Sun, 21 Jun 2020 22:07:44: 15000000 INFO @ Sun, 21 Jun 2020 22:07:47: 5000000 INFO @ Sun, 21 Jun 2020 22:07:48: 10000000 INFO @ Sun, 21 Jun 2020 22:07:51: 16000000 INFO @ Sun, 21 Jun 2020 22:07:54: 6000000 INFO @ Sun, 21 Jun 2020 22:07:54: 11000000 INFO @ Sun, 21 Jun 2020 22:07:57: 17000000 INFO @ Sun, 21 Jun 2020 22:08:00: 7000000 INFO @ Sun, 21 Jun 2020 22:08:00: 12000000 INFO @ Sun, 21 Jun 2020 22:08:03: 18000000 INFO @ Sun, 21 Jun 2020 22:08:06: 8000000 INFO @ Sun, 21 Jun 2020 22:08:07: 13000000 INFO @ Sun, 21 Jun 2020 22:08:09: 19000000 INFO @ Sun, 21 Jun 2020 22:08:12: 9000000 INFO @ Sun, 21 Jun 2020 22:08:13: 14000000 INFO @ Sun, 21 Jun 2020 22:08:16: 20000000 INFO @ Sun, 21 Jun 2020 22:08:19: 10000000 INFO @ Sun, 21 Jun 2020 22:08:19: 15000000 INFO @ Sun, 21 Jun 2020 22:08:22: 21000000 INFO @ Sun, 21 Jun 2020 22:08:25: 11000000 INFO @ Sun, 21 Jun 2020 22:08:26: 16000000 INFO @ Sun, 21 Jun 2020 22:08:28: 22000000 INFO @ Sun, 21 Jun 2020 22:08:32: 12000000 INFO @ Sun, 21 Jun 2020 22:08:32: 17000000 INFO @ Sun, 21 Jun 2020 22:08:35: 23000000 INFO @ Sun, 21 Jun 2020 22:08:38: 13000000 INFO @ Sun, 21 Jun 2020 22:08:38: 18000000 INFO @ Sun, 21 Jun 2020 22:08:41: 24000000 INFO @ Sun, 21 Jun 2020 22:08:44: 14000000 INFO @ Sun, 21 Jun 2020 22:08:45: 19000000 INFO @ Sun, 21 Jun 2020 22:08:47: 25000000 INFO @ Sun, 21 Jun 2020 22:08:51: 15000000 INFO @ Sun, 21 Jun 2020 22:08:51: 20000000 INFO @ Sun, 21 Jun 2020 22:08:54: 26000000 INFO @ Sun, 21 Jun 2020 22:08:57: 16000000 INFO @ Sun, 21 Jun 2020 22:08:57: 21000000 INFO @ Sun, 21 Jun 2020 22:09:00: 27000000 INFO @ Sun, 21 Jun 2020 22:09:04: 22000000 INFO @ Sun, 21 Jun 2020 22:09:04: 17000000 INFO @ Sun, 21 Jun 2020 22:09:07: 28000000 INFO @ Sun, 21 Jun 2020 22:09:10: 23000000 INFO @ Sun, 21 Jun 2020 22:09:11: 18000000 INFO @ Sun, 21 Jun 2020 22:09:13: 29000000 INFO @ Sun, 21 Jun 2020 22:09:17: 24000000 INFO @ Sun, 21 Jun 2020 22:09:17: 19000000 INFO @ Sun, 21 Jun 2020 22:09:20: 30000000 INFO @ Sun, 21 Jun 2020 22:09:23: 25000000 INFO @ Sun, 21 Jun 2020 22:09:23: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:09:26: 31000000 INFO @ Sun, 21 Jun 2020 22:09:29: 26000000 INFO @ Sun, 21 Jun 2020 22:09:30: 21000000 INFO @ Sun, 21 Jun 2020 22:09:32: 32000000 INFO @ Sun, 21 Jun 2020 22:09:35: 27000000 INFO @ Sun, 21 Jun 2020 22:09:36: 22000000 INFO @ Sun, 21 Jun 2020 22:09:39: 33000000 INFO @ Sun, 21 Jun 2020 22:09:42: 28000000 INFO @ Sun, 21 Jun 2020 22:09:43: 23000000 INFO @ Sun, 21 Jun 2020 22:09:45: 34000000 INFO @ Sun, 21 Jun 2020 22:09:49: 29000000 INFO @ Sun, 21 Jun 2020 22:09:49: 24000000 INFO @ Sun, 21 Jun 2020 22:09:52: 35000000 INFO @ Sun, 21 Jun 2020 22:09:55: 30000000 INFO @ Sun, 21 Jun 2020 22:09:56: 25000000 INFO @ Sun, 21 Jun 2020 22:09:58: 36000000 INFO @ Sun, 21 Jun 2020 22:10:01: 31000000 INFO @ Sun, 21 Jun 2020 22:10:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:10:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:10:02: #1 total tags in treatment: 36562359 INFO @ Sun, 21 Jun 2020 22:10:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:02: #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 22:10:02: 26000000 INFO @ Sun, 21 Jun 2020 22:10:03: #1 tags after filtering in treatment: 36562331 INFO @ Sun, 21 Jun 2020 22:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:03: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:05: #2 number of paired peaks: 3417 INFO @ Sun, 21 Jun 2020 22:10:05: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:06: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:06: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:06: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:06: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:10:06: #2 alternative fragment length(s) may be 1,81,96,121 bps INFO @ Sun, 21 Jun 2020 22:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.05_model.r WARNING @ Sun, 21 Jun 2020 22:10:06: #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 22:10:06: #2 You may need to consider one of the other alternative d(s): 1,81,96,121 WARNING @ Sun, 21 Jun 2020 22:10:06: #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 22:10:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:08: 32000000 INFO @ Sun, 21 Jun 2020 22:10:09: 27000000 INFO @ Sun, 21 Jun 2020 22:10:14: 33000000 INFO @ Sun, 21 Jun 2020 22:10:15: 28000000 INFO @ Sun, 21 Jun 2020 22:10:20: 34000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:10:22: 29000000 INFO @ Sun, 21 Jun 2020 22:10:27: 35000000 INFO @ Sun, 21 Jun 2020 22:10:28: 30000000 INFO @ Sun, 21 Jun 2020 22:10:33: 36000000 INFO @ Sun, 21 Jun 2020 22:10:35: 31000000 INFO @ Sun, 21 Jun 2020 22:10:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:10:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:10:37: #1 total tags in treatment: 36562359 INFO @ Sun, 21 Jun 2020 22:10:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:37: #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 22:10:38: #1 tags after filtering in treatment: 36562331 INFO @ Sun, 21 Jun 2020 22:10:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:38: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:40: #2 number of paired peaks: 3417 INFO @ Sun, 21 Jun 2020 22:10:40: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:41: 32000000 INFO @ Sun, 21 Jun 2020 22:10:41: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:41: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:41: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:41: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:10:41: #2 alternative fragment length(s) may be 1,81,96,121 bps INFO @ Sun, 21 Jun 2020 22:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.10_model.r WARNING @ Sun, 21 Jun 2020 22:10:41: #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 22:10:41: #2 You may need to consider one of the other alternative d(s): 1,81,96,121 WARNING @ Sun, 21 Jun 2020 22:10:41: #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 22:10:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:46: 33000000 INFO @ Sun, 21 Jun 2020 22:10:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:52: 34000000 INFO @ Sun, 21 Jun 2020 22:10:58: 35000000 INFO @ Sun, 21 Jun 2020 22:11:04: 36000000 INFO @ Sun, 21 Jun 2020 22:11:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:11:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:11:07: #1 total tags in treatment: 36562359 INFO @ Sun, 21 Jun 2020 22:11:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:07: #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 22:11:08: #1 tags after filtering in treatment: 36562331 INFO @ Sun, 21 Jun 2020 22:11:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:08: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.05_summits.bed INFO @ Sun, 21 Jun 2020 22:11:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:11: #2 number of paired peaks: 3417 INFO @ Sun, 21 Jun 2020 22:11:11: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:11: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:11: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:11: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:11: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:11:11: #2 alternative fragment length(s) may be 1,81,96,121 bps INFO @ Sun, 21 Jun 2020 22:11:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.20_model.r WARNING @ Sun, 21 Jun 2020 22:11:11: #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 22:11:11: #2 You may need to consider one of the other alternative d(s): 1,81,96,121 WARNING @ Sun, 21 Jun 2020 22:11:11: #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 22:11:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.10_summits.bed INFO @ Sun, 21 Jun 2020 22:11:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923197/SRX4923197.20_summits.bed INFO @ Sun, 21 Jun 2020 22:12:12: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling