Job ID = 6457040 SRX = SRX4370070 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:31:25 prefetch.2.10.7: 1) Downloading 'SRR7500647'... 2020-06-21T11:31:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:35:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:35:38 prefetch.2.10.7: 1) 'SRR7500647' was downloaded successfully 2020-06-21T11:35:38 prefetch.2.10.7: 'SRR7500647' has 0 unresolved dependencies Read 75434220 spots for SRR7500647/SRR7500647.sra Written 75434220 spots for SRR7500647/SRR7500647.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: 00:20:39 75434220 reads; of these: 75434220 (100.00%) were unpaired; of these: 2053781 (2.72%) aligned 0 times 55878345 (74.08%) aligned exactly 1 time 17502094 (23.20%) aligned >1 times 97.28% overall alignment rate Time searching: 00:20:39 Overall time: 00:20:39 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] 38165934 / 73380439 = 0.5201 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 21:10:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.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 21:10:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:10:41: 1000000 INFO @ Sun, 21 Jun 2020 21:10:47: 2000000 INFO @ Sun, 21 Jun 2020 21:10:52: 3000000 INFO @ Sun, 21 Jun 2020 21:10:57: 4000000 INFO @ Sun, 21 Jun 2020 21:11:03: 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 21:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.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 21:11:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:08: 6000000 INFO @ Sun, 21 Jun 2020 21:11:12: 1000000 INFO @ Sun, 21 Jun 2020 21:11:15: 7000000 INFO @ Sun, 21 Jun 2020 21:11:18: 2000000 INFO @ Sun, 21 Jun 2020 21:11:20: 8000000 INFO @ Sun, 21 Jun 2020 21:11:25: 3000000 INFO @ Sun, 21 Jun 2020 21:11:26: 9000000 INFO @ Sun, 21 Jun 2020 21:11:31: 4000000 INFO @ Sun, 21 Jun 2020 21:11:32: 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 21:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.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 21:11:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:11:37: 11000000 INFO @ Sun, 21 Jun 2020 21:11:37: 5000000 INFO @ Sun, 21 Jun 2020 21:11:41: 1000000 INFO @ Sun, 21 Jun 2020 21:11:43: 12000000 INFO @ Sun, 21 Jun 2020 21:11:44: 6000000 INFO @ Sun, 21 Jun 2020 21:11:47: 2000000 INFO @ Sun, 21 Jun 2020 21:11:50: 13000000 INFO @ Sun, 21 Jun 2020 21:11:50: 7000000 INFO @ Sun, 21 Jun 2020 21:11:53: 3000000 INFO @ Sun, 21 Jun 2020 21:11:55: 14000000 INFO @ Sun, 21 Jun 2020 21:11:57: 8000000 INFO @ Sun, 21 Jun 2020 21:11:58: 4000000 INFO @ Sun, 21 Jun 2020 21:12:01: 15000000 INFO @ Sun, 21 Jun 2020 21:12:03: 9000000 INFO @ Sun, 21 Jun 2020 21:12:04: 5000000 INFO @ Sun, 21 Jun 2020 21:12:07: 16000000 INFO @ Sun, 21 Jun 2020 21:12:09: 10000000 INFO @ Sun, 21 Jun 2020 21:12:09: 6000000 INFO @ Sun, 21 Jun 2020 21:12:12: 17000000 INFO @ Sun, 21 Jun 2020 21:12:15: 7000000 INFO @ Sun, 21 Jun 2020 21:12:15: 11000000 INFO @ Sun, 21 Jun 2020 21:12:18: 18000000 INFO @ Sun, 21 Jun 2020 21:12:21: 8000000 INFO @ Sun, 21 Jun 2020 21:12:21: 12000000 INFO @ Sun, 21 Jun 2020 21:12:24: 19000000 INFO @ Sun, 21 Jun 2020 21:12:26: 9000000 INFO @ Sun, 21 Jun 2020 21:12:27: 13000000 INFO @ Sun, 21 Jun 2020 21:12:29: 20000000 INFO @ Sun, 21 Jun 2020 21:12:32: 10000000 INFO @ Sun, 21 Jun 2020 21:12:34: 14000000 INFO @ Sun, 21 Jun 2020 21:12:35: 21000000 INFO @ Sun, 21 Jun 2020 21:12:38: 11000000 INFO @ Sun, 21 Jun 2020 21:12:40: 15000000 INFO @ Sun, 21 Jun 2020 21:12:41: 22000000 INFO @ Sun, 21 Jun 2020 21:12:43: 12000000 INFO @ Sun, 21 Jun 2020 21:12:46: 16000000 INFO @ Sun, 21 Jun 2020 21:12:46: 23000000 INFO @ Sun, 21 Jun 2020 21:12:49: 13000000 INFO @ Sun, 21 Jun 2020 21:12:52: 24000000 INFO @ Sun, 21 Jun 2020 21:12:52: 17000000 INFO @ Sun, 21 Jun 2020 21:12:54: 14000000 INFO @ Sun, 21 Jun 2020 21:12:57: 25000000 INFO @ Sun, 21 Jun 2020 21:12:58: 18000000 INFO @ Sun, 21 Jun 2020 21:13:00: 15000000 INFO @ Sun, 21 Jun 2020 21:13:03: 26000000 INFO @ Sun, 21 Jun 2020 21:13:04: 19000000 INFO @ Sun, 21 Jun 2020 21:13:06: 16000000 INFO @ Sun, 21 Jun 2020 21:13:09: 27000000 INFO @ Sun, 21 Jun 2020 21:13:10: 20000000 INFO @ Sun, 21 Jun 2020 21:13:11: 17000000 INFO @ Sun, 21 Jun 2020 21:13:14: 28000000 INFO @ Sun, 21 Jun 2020 21:13:17: 21000000 INFO @ Sun, 21 Jun 2020 21:13:17: 18000000 INFO @ Sun, 21 Jun 2020 21:13:20: 29000000 INFO @ Sun, 21 Jun 2020 21:13:23: 19000000 INFO @ Sun, 21 Jun 2020 21:13:23: 22000000 INFO @ Sun, 21 Jun 2020 21:13:26: 30000000 INFO @ Sun, 21 Jun 2020 21:13:28: 20000000 INFO @ Sun, 21 Jun 2020 21:13:29: 23000000 INFO @ Sun, 21 Jun 2020 21:13:32: 31000000 INFO @ Sun, 21 Jun 2020 21:13:34: 21000000 INFO @ Sun, 21 Jun 2020 21:13:35: 24000000 INFO @ Sun, 21 Jun 2020 21:13:38: 32000000 INFO @ Sun, 21 Jun 2020 21:13:39: 22000000 INFO @ Sun, 21 Jun 2020 21:13:41: 25000000 INFO @ Sun, 21 Jun 2020 21:13:44: 33000000 INFO @ Sun, 21 Jun 2020 21:13:45: 23000000 INFO @ Sun, 21 Jun 2020 21:13:47: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:13:51: 24000000 INFO @ Sun, 21 Jun 2020 21:13:51: 34000000 INFO @ Sun, 21 Jun 2020 21:13:53: 27000000 INFO @ Sun, 21 Jun 2020 21:13:56: 25000000 INFO @ Sun, 21 Jun 2020 21:13:59: 35000000 INFO @ Sun, 21 Jun 2020 21:14:00: 28000000 INFO @ Sun, 21 Jun 2020 21:14:00: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:14:00: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:14:00: #1 total tags in treatment: 35214505 INFO @ Sun, 21 Jun 2020 21:14:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:00: #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 21:14:01: #1 tags after filtering in treatment: 35214448 INFO @ Sun, 21 Jun 2020 21:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:01: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:02: 26000000 INFO @ Sun, 21 Jun 2020 21:14:04: #2 number of paired peaks: 3332 INFO @ Sun, 21 Jun 2020 21:14:04: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:04: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:04: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:04: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:04: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 21:14:04: #2 alternative fragment length(s) may be 1,38 bps INFO @ Sun, 21 Jun 2020 21:14:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.05_model.r WARNING @ Sun, 21 Jun 2020 21:14:04: #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 21:14:04: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Sun, 21 Jun 2020 21:14:04: #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 21:14:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:14:06: 29000000 INFO @ Sun, 21 Jun 2020 21:14:07: 27000000 INFO @ Sun, 21 Jun 2020 21:14:13: 30000000 INFO @ Sun, 21 Jun 2020 21:14:13: 28000000 INFO @ Sun, 21 Jun 2020 21:14:19: 29000000 INFO @ Sun, 21 Jun 2020 21:14:19: 31000000 INFO @ Sun, 21 Jun 2020 21:14:25: 30000000 INFO @ Sun, 21 Jun 2020 21:14:26: 32000000 INFO @ Sun, 21 Jun 2020 21:14:30: 31000000 INFO @ Sun, 21 Jun 2020 21:14:32: 33000000 INFO @ Sun, 21 Jun 2020 21:14:36: 32000000 INFO @ Sun, 21 Jun 2020 21:14:38: 34000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:14:42: 33000000 INFO @ Sun, 21 Jun 2020 21:14:45: 35000000 INFO @ Sun, 21 Jun 2020 21:14:46: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:14:46: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:14:46: #1 total tags in treatment: 35214505 INFO @ Sun, 21 Jun 2020 21:14:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:46: #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 21:14:47: 34000000 INFO @ Sun, 21 Jun 2020 21:14:47: #1 tags after filtering in treatment: 35214448 INFO @ Sun, 21 Jun 2020 21:14:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:47: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:50: #2 number of paired peaks: 3332 INFO @ Sun, 21 Jun 2020 21:14:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:50: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 21:14:50: #2 alternative fragment length(s) may be 1,38 bps INFO @ Sun, 21 Jun 2020 21:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.10_model.r WARNING @ Sun, 21 Jun 2020 21:14:50: #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 21:14:50: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Sun, 21 Jun 2020 21:14:50: #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 21:14:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:14:53: 35000000 INFO @ Sun, 21 Jun 2020 21:14:54: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:14:54: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:14:54: #1 total tags in treatment: 35214505 INFO @ Sun, 21 Jun 2020 21:14:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:54: #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 21:14:55: #1 tags after filtering in treatment: 35214448 INFO @ Sun, 21 Jun 2020 21:14:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:57: #2 number of paired peaks: 3332 INFO @ Sun, 21 Jun 2020 21:14:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:58: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:58: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:58: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:58: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 21:14:58: #2 alternative fragment length(s) may be 1,38 bps INFO @ Sun, 21 Jun 2020 21:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.20_model.r WARNING @ Sun, 21 Jun 2020 21:14:58: #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 21:14:58: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Sun, 21 Jun 2020 21:14:58: #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 21:14:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:15:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.05_summits.bed INFO @ Sun, 21 Jun 2020 21:15:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:15:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.10_summits.bed INFO @ Sun, 21 Jun 2020 21:15:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370070/SRX4370070.20_summits.bed INFO @ Sun, 21 Jun 2020 21:15:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling