Job ID = 6453679 SRX = SRX1361348 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:33:09 prefetch.2.10.7: 1) Downloading 'SRR2749786'... 2020-06-21T08:33:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:41:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:41:20 prefetch.2.10.7: 1) 'SRR2749786' was downloaded successfully Read 60988969 spots for SRR2749786/SRR2749786.sra Written 60988969 spots for SRR2749786/SRR2749786.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: 00:25:40 60988969 reads; of these: 60988969 (100.00%) were unpaired; of these: 2186801 (3.59%) aligned 0 times 23391227 (38.35%) aligned exactly 1 time 35410941 (58.06%) aligned >1 times 96.41% overall alignment rate Time searching: 00:25:40 Overall time: 00:25:40 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 24 files... [bam_rmdupse_core] 27897431 / 58802168 = 0.4744 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 18:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.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 18:25:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:28: 1000000 INFO @ Sun, 21 Jun 2020 18:25:37: 2000000 INFO @ Sun, 21 Jun 2020 18:25:46: 3000000 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 18:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.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 18:25:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:54: 4000000 INFO @ Sun, 21 Jun 2020 18:25:58: 1000000 INFO @ Sun, 21 Jun 2020 18:26:03: 5000000 INFO @ Sun, 21 Jun 2020 18:26:07: 2000000 INFO @ Sun, 21 Jun 2020 18:26:11: 6000000 INFO @ Sun, 21 Jun 2020 18:26:15: 3000000 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 18:26:20: 7000000 INFO @ Sun, 21 Jun 2020 18:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.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 18:26:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:23: 4000000 INFO @ Sun, 21 Jun 2020 18:26:29: 8000000 INFO @ Sun, 21 Jun 2020 18:26:30: 1000000 INFO @ Sun, 21 Jun 2020 18:26:31: 5000000 INFO @ Sun, 21 Jun 2020 18:26:38: 9000000 INFO @ Sun, 21 Jun 2020 18:26:39: 2000000 INFO @ Sun, 21 Jun 2020 18:26:39: 6000000 INFO @ Sun, 21 Jun 2020 18:26:47: 7000000 INFO @ Sun, 21 Jun 2020 18:26:47: 10000000 INFO @ Sun, 21 Jun 2020 18:26:47: 3000000 INFO @ Sun, 21 Jun 2020 18:26:54: 8000000 INFO @ Sun, 21 Jun 2020 18:26:55: 11000000 INFO @ Sun, 21 Jun 2020 18:26:56: 4000000 INFO @ Sun, 21 Jun 2020 18:27:01: 9000000 INFO @ Sun, 21 Jun 2020 18:27:04: 12000000 INFO @ Sun, 21 Jun 2020 18:27:05: 5000000 INFO @ Sun, 21 Jun 2020 18:27:09: 10000000 INFO @ Sun, 21 Jun 2020 18:27:13: 13000000 INFO @ Sun, 21 Jun 2020 18:27:14: 6000000 INFO @ Sun, 21 Jun 2020 18:27:16: 11000000 INFO @ Sun, 21 Jun 2020 18:27:21: 14000000 INFO @ Sun, 21 Jun 2020 18:27:22: 7000000 INFO @ Sun, 21 Jun 2020 18:27:24: 12000000 INFO @ Sun, 21 Jun 2020 18:27:29: 15000000 INFO @ Sun, 21 Jun 2020 18:27:30: 8000000 INFO @ Sun, 21 Jun 2020 18:27:31: 13000000 INFO @ Sun, 21 Jun 2020 18:27:37: 16000000 INFO @ Sun, 21 Jun 2020 18:27:37: 9000000 INFO @ Sun, 21 Jun 2020 18:27:39: 14000000 INFO @ Sun, 21 Jun 2020 18:27:45: 17000000 INFO @ Sun, 21 Jun 2020 18:27:45: 10000000 INFO @ Sun, 21 Jun 2020 18:27:46: 15000000 INFO @ Sun, 21 Jun 2020 18:27:53: 18000000 INFO @ Sun, 21 Jun 2020 18:27:53: 16000000 INFO @ Sun, 21 Jun 2020 18:27:53: 11000000 INFO @ Sun, 21 Jun 2020 18:28:00: 17000000 INFO @ Sun, 21 Jun 2020 18:28:01: 19000000 INFO @ Sun, 21 Jun 2020 18:28:01: 12000000 INFO @ Sun, 21 Jun 2020 18:28:08: 18000000 INFO @ Sun, 21 Jun 2020 18:28:08: 13000000 INFO @ Sun, 21 Jun 2020 18:28:09: 20000000 INFO @ Sun, 21 Jun 2020 18:28:15: 19000000 INFO @ Sun, 21 Jun 2020 18:28:16: 14000000 INFO @ Sun, 21 Jun 2020 18:28:17: 21000000 INFO @ Sun, 21 Jun 2020 18:28:22: 20000000 INFO @ Sun, 21 Jun 2020 18:28:24: 15000000 INFO @ Sun, 21 Jun 2020 18:28:25: 22000000 INFO @ Sun, 21 Jun 2020 18:28:30: 21000000 INFO @ Sun, 21 Jun 2020 18:28:32: 16000000 INFO @ Sun, 21 Jun 2020 18:28:33: 23000000 INFO @ Sun, 21 Jun 2020 18:28:37: 22000000 INFO @ Sun, 21 Jun 2020 18:28:39: 17000000 INFO @ Sun, 21 Jun 2020 18:28:41: 24000000 INFO @ Sun, 21 Jun 2020 18:28:44: 23000000 INFO @ Sun, 21 Jun 2020 18:28:47: 18000000 INFO @ Sun, 21 Jun 2020 18:28:49: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:28:52: 24000000 INFO @ Sun, 21 Jun 2020 18:28:54: 19000000 INFO @ Sun, 21 Jun 2020 18:28:56: 26000000 INFO @ Sun, 21 Jun 2020 18:28:59: 25000000 INFO @ Sun, 21 Jun 2020 18:29:02: 20000000 INFO @ Sun, 21 Jun 2020 18:29:04: 27000000 INFO @ Sun, 21 Jun 2020 18:29:06: 26000000 INFO @ Sun, 21 Jun 2020 18:29:09: 21000000 INFO @ Sun, 21 Jun 2020 18:29:12: 28000000 INFO @ Sun, 21 Jun 2020 18:29:14: 27000000 INFO @ Sun, 21 Jun 2020 18:29:17: 22000000 INFO @ Sun, 21 Jun 2020 18:29:19: 29000000 INFO @ Sun, 21 Jun 2020 18:29:21: 28000000 INFO @ Sun, 21 Jun 2020 18:29:24: 23000000 INFO @ Sun, 21 Jun 2020 18:29:27: 30000000 INFO @ Sun, 21 Jun 2020 18:29:28: 29000000 INFO @ Sun, 21 Jun 2020 18:29:32: 24000000 INFO @ Sun, 21 Jun 2020 18:29:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:29:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:29:34: #1 total tags in treatment: 30904737 INFO @ Sun, 21 Jun 2020 18:29:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:29:34: #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 18:29:35: #1 tags after filtering in treatment: 30904702 INFO @ Sun, 21 Jun 2020 18:29:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:36: 30000000 INFO @ Sun, 21 Jun 2020 18:29:38: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 18:29:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:38: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:29:38: #2 alternative fragment length(s) may be 1,38 bps INFO @ Sun, 21 Jun 2020 18:29:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.05_model.r WARNING @ Sun, 21 Jun 2020 18:29:38: #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 18:29:38: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Sun, 21 Jun 2020 18:29:38: #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 18:29:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:29:39: 25000000 INFO @ Sun, 21 Jun 2020 18:29:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:29:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:29:43: #1 total tags in treatment: 30904737 INFO @ Sun, 21 Jun 2020 18:29:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:29:43: #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 18:29:44: #1 tags after filtering in treatment: 30904702 INFO @ Sun, 21 Jun 2020 18:29:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:45: 26000000 INFO @ Sun, 21 Jun 2020 18:29:46: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 18:29:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:46: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:29:46: #2 alternative fragment length(s) may be 1,38 bps INFO @ Sun, 21 Jun 2020 18:29:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.10_model.r WARNING @ Sun, 21 Jun 2020 18:29:46: #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 18:29:46: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Sun, 21 Jun 2020 18:29:46: #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 18:29:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:29:52: 27000000 INFO @ Sun, 21 Jun 2020 18:29:59: 28000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:30:05: 29000000 INFO @ Sun, 21 Jun 2020 18:30:12: 30000000 INFO @ Sun, 21 Jun 2020 18:30:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:30:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:30:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:30:19: #1 total tags in treatment: 30904737 INFO @ Sun, 21 Jun 2020 18:30:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:19: #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 18:30:20: #1 tags after filtering in treatment: 30904702 INFO @ Sun, 21 Jun 2020 18:30:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:20: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:22: #2 number of paired peaks: 2557 INFO @ Sun, 21 Jun 2020 18:30:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:30:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:23: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:30:23: #2 alternative fragment length(s) may be 1,38 bps INFO @ Sun, 21 Jun 2020 18:30:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.20_model.r WARNING @ Sun, 21 Jun 2020 18:30:23: #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 18:30:23: #2 You may need to consider one of the other alternative d(s): 1,38 WARNING @ Sun, 21 Jun 2020 18:30:23: #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 18:30:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:30:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:30:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.05_summits.bed INFO @ Sun, 21 Jun 2020 18:30:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:30:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:30:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:30:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.10_summits.bed INFO @ Sun, 21 Jun 2020 18:30:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:31:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1361348/SRX1361348.20_summits.bed INFO @ Sun, 21 Jun 2020 18:31:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling