Job ID = 6497713 SRX = SRX1056724 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:29:27 prefetch.2.10.7: 1) Downloading 'SRR2060658'... 2020-06-25T22:29:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:03:23 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:03:23 prefetch.2.10.7: 1) 'SRR2060658' was downloaded successfully Read 90015801 spots for SRR2060658/SRR2060658.sra Written 90015801 spots for SRR2060658/SRR2060658.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: 04:21:27 90015801 reads; of these: 90015801 (100.00%) were paired; of these: 22908638 (25.45%) aligned concordantly 0 times 49284989 (54.75%) aligned concordantly exactly 1 time 17822174 (19.80%) aligned concordantly >1 times ---- 22908638 pairs aligned concordantly 0 times; of these: 772048 (3.37%) aligned discordantly 1 time ---- 22136590 pairs aligned 0 times concordantly or discordantly; of these: 44273180 mates make up the pairs; of these: 41005368 (92.62%) aligned 0 times 1996602 (4.51%) aligned exactly 1 time 1271210 (2.87%) aligned >1 times 77.22% overall alignment rate Time searching: 04:21:27 Overall time: 04:21:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 60 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 53199316 / 67712571 = 0.7857 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 @ Fri, 26 Jun 2020 13:25:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.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 @ Fri, 26 Jun 2020 13:25:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 13:25:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 13:25:38: 1000000 INFO @ Fri, 26 Jun 2020 13:25:46: 2000000 INFO @ Fri, 26 Jun 2020 13:25:54: 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 @ Fri, 26 Jun 2020 13:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.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 @ Fri, 26 Jun 2020 13:26:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 13:26:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 13:26:03: 4000000 INFO @ Fri, 26 Jun 2020 13:26:09: 1000000 INFO @ Fri, 26 Jun 2020 13:26:12: 5000000 INFO @ Fri, 26 Jun 2020 13:26:18: 2000000 INFO @ Fri, 26 Jun 2020 13:26:21: 6000000 INFO @ Fri, 26 Jun 2020 13:26:28: 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 @ Fri, 26 Jun 2020 13:26:29: 7000000 INFO @ Fri, 26 Jun 2020 13:26:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.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 @ Fri, 26 Jun 2020 13:26:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 13:26:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 13:26:37: 4000000 INFO @ Fri, 26 Jun 2020 13:26:39: 8000000 INFO @ Fri, 26 Jun 2020 13:26:39: 1000000 INFO @ Fri, 26 Jun 2020 13:26:46: 5000000 INFO @ Fri, 26 Jun 2020 13:26:48: 9000000 INFO @ Fri, 26 Jun 2020 13:26:48: 2000000 INFO @ Fri, 26 Jun 2020 13:26:55: 6000000 INFO @ Fri, 26 Jun 2020 13:26:57: 10000000 INFO @ Fri, 26 Jun 2020 13:26:58: 3000000 INFO @ Fri, 26 Jun 2020 13:27:04: 7000000 INFO @ Fri, 26 Jun 2020 13:27:05: 11000000 INFO @ Fri, 26 Jun 2020 13:27:07: 4000000 INFO @ Fri, 26 Jun 2020 13:27:14: 8000000 INFO @ Fri, 26 Jun 2020 13:27:14: 12000000 INFO @ Fri, 26 Jun 2020 13:27:16: 5000000 INFO @ Fri, 26 Jun 2020 13:27:23: 13000000 INFO @ Fri, 26 Jun 2020 13:27:23: 9000000 INFO @ Fri, 26 Jun 2020 13:27:25: 6000000 INFO @ Fri, 26 Jun 2020 13:27:32: 10000000 INFO @ Fri, 26 Jun 2020 13:27:32: 14000000 INFO @ Fri, 26 Jun 2020 13:27:34: 7000000 INFO @ Fri, 26 Jun 2020 13:27:40: 11000000 INFO @ Fri, 26 Jun 2020 13:27:41: 15000000 INFO @ Fri, 26 Jun 2020 13:27:44: 8000000 INFO @ Fri, 26 Jun 2020 13:27:49: 12000000 INFO @ Fri, 26 Jun 2020 13:27:51: 16000000 INFO @ Fri, 26 Jun 2020 13:27:53: 9000000 INFO @ Fri, 26 Jun 2020 13:27:58: 13000000 INFO @ Fri, 26 Jun 2020 13:28:00: 17000000 INFO @ Fri, 26 Jun 2020 13:28:01: 10000000 INFO @ Fri, 26 Jun 2020 13:28:08: 14000000 INFO @ Fri, 26 Jun 2020 13:28:10: 18000000 INFO @ Fri, 26 Jun 2020 13:28:10: 11000000 INFO @ Fri, 26 Jun 2020 13:28:17: 15000000 INFO @ Fri, 26 Jun 2020 13:28:19: 12000000 INFO @ Fri, 26 Jun 2020 13:28:19: 19000000 INFO @ Fri, 26 Jun 2020 13:28:27: 16000000 INFO @ Fri, 26 Jun 2020 13:28:28: 13000000 INFO @ Fri, 26 Jun 2020 13:28:29: 20000000 INFO @ Fri, 26 Jun 2020 13:28:37: 17000000 INFO @ Fri, 26 Jun 2020 13:28:37: 14000000 INFO @ Fri, 26 Jun 2020 13:28:39: 21000000 INFO @ Fri, 26 Jun 2020 13:28:46: 15000000 INFO @ Fri, 26 Jun 2020 13:28:46: 18000000 INFO @ Fri, 26 Jun 2020 13:28:48: 22000000 INFO @ Fri, 26 Jun 2020 13:28:55: 16000000 INFO @ Fri, 26 Jun 2020 13:28:56: 19000000 INFO @ Fri, 26 Jun 2020 13:28:58: 23000000 INFO @ Fri, 26 Jun 2020 13:29:05: 17000000 INFO @ Fri, 26 Jun 2020 13:29:07: 20000000 INFO @ Fri, 26 Jun 2020 13:29:08: 24000000 INFO @ Fri, 26 Jun 2020 13:29:14: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 13:29:17: 21000000 INFO @ Fri, 26 Jun 2020 13:29:19: 25000000 INFO @ Fri, 26 Jun 2020 13:29:24: 19000000 INFO @ Fri, 26 Jun 2020 13:29:27: 22000000 INFO @ Fri, 26 Jun 2020 13:29:29: 26000000 INFO @ Fri, 26 Jun 2020 13:29:33: 20000000 INFO @ Fri, 26 Jun 2020 13:29:38: 23000000 INFO @ Fri, 26 Jun 2020 13:29:39: 27000000 INFO @ Fri, 26 Jun 2020 13:29:42: 21000000 INFO @ Fri, 26 Jun 2020 13:29:48: 24000000 INFO @ Fri, 26 Jun 2020 13:29:49: 28000000 INFO @ Fri, 26 Jun 2020 13:29:52: 22000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 13:29:58: 25000000 INFO @ Fri, 26 Jun 2020 13:30:00: 29000000 INFO @ Fri, 26 Jun 2020 13:30:02: 23000000 INFO @ Fri, 26 Jun 2020 13:30:09: 26000000 INFO @ Fri, 26 Jun 2020 13:30:10: 30000000 INFO @ Fri, 26 Jun 2020 13:30:11: 24000000 INFO @ Fri, 26 Jun 2020 13:30:19: 27000000 INFO @ Fri, 26 Jun 2020 13:30:20: 31000000 INFO @ Fri, 26 Jun 2020 13:30:21: 25000000 INFO @ Fri, 26 Jun 2020 13:30:30: 28000000 INFO @ Fri, 26 Jun 2020 13:30:30: 26000000 INFO @ Fri, 26 Jun 2020 13:30:31: 32000000 INFO @ Fri, 26 Jun 2020 13:30:37: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 13:30:37: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 13:30:37: #1 total tags in treatment: 14541965 INFO @ Fri, 26 Jun 2020 13:30:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 13:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 13:30:37: #1 tags after filtering in treatment: 11186453 INFO @ Fri, 26 Jun 2020 13:30:37: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 13:30:37: #1 finished! INFO @ Fri, 26 Jun 2020 13:30:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 13:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 13:30:39: #2 number of paired peaks: 6080 INFO @ Fri, 26 Jun 2020 13:30:39: start model_add_line... INFO @ Fri, 26 Jun 2020 13:30:39: start X-correlation... INFO @ Fri, 26 Jun 2020 13:30:39: end of X-cor INFO @ Fri, 26 Jun 2020 13:30:39: #2 finished! INFO @ Fri, 26 Jun 2020 13:30:39: #2 predicted fragment length is 176 bps INFO @ Fri, 26 Jun 2020 13:30:39: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 26 Jun 2020 13:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.05_model.r WARNING @ Fri, 26 Jun 2020 13:30:39: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 13:30:39: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 26 Jun 2020 13:30:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 13:30:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 13:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 13:30:39: 29000000 INFO @ Fri, 26 Jun 2020 13:30:40: 27000000 INFO @ Fri, 26 Jun 2020 13:30:49: 30000000 INFO @ Fri, 26 Jun 2020 13:30:50: 28000000 INFO @ Fri, 26 Jun 2020 13:30:58: 31000000 INFO @ Fri, 26 Jun 2020 13:31:00: 29000000 INFO @ Fri, 26 Jun 2020 13:31:08: 32000000 INFO @ Fri, 26 Jun 2020 13:31:09: 30000000 INFO @ Fri, 26 Jun 2020 13:31:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 13:31:14: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 13:31:14: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 13:31:14: #1 total tags in treatment: 14541965 INFO @ Fri, 26 Jun 2020 13:31:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 13:31:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 13:31:14: #1 tags after filtering in treatment: 11186453 INFO @ Fri, 26 Jun 2020 13:31:14: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 13:31:14: #1 finished! INFO @ Fri, 26 Jun 2020 13:31:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 13:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 13:31:15: #2 number of paired peaks: 6080 INFO @ Fri, 26 Jun 2020 13:31:15: start model_add_line... INFO @ Fri, 26 Jun 2020 13:31:16: start X-correlation... INFO @ Fri, 26 Jun 2020 13:31:16: end of X-cor INFO @ Fri, 26 Jun 2020 13:31:16: #2 finished! INFO @ Fri, 26 Jun 2020 13:31:16: #2 predicted fragment length is 176 bps INFO @ Fri, 26 Jun 2020 13:31:16: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 26 Jun 2020 13:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.10_model.r WARNING @ Fri, 26 Jun 2020 13:31:16: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 13:31:16: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 26 Jun 2020 13:31:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 13:31:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 13:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 13:31:19: 31000000 INFO @ Fri, 26 Jun 2020 13:31:27: 32000000 INFO @ Fri, 26 Jun 2020 13:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.05_peaks.xls INFO @ Fri, 26 Jun 2020 13:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 13:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.05_summits.bed INFO @ Fri, 26 Jun 2020 13:31:29: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15210 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 13:31:33: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 13:31:33: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 13:31:33: #1 total tags in treatment: 14541965 INFO @ Fri, 26 Jun 2020 13:31:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 13:31:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 13:31:33: #1 tags after filtering in treatment: 11186453 INFO @ Fri, 26 Jun 2020 13:31:33: #1 Redundant rate of treatment: 0.23 INFO @ Fri, 26 Jun 2020 13:31:33: #1 finished! INFO @ Fri, 26 Jun 2020 13:31:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 13:31:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 13:31:35: #2 number of paired peaks: 6080 INFO @ Fri, 26 Jun 2020 13:31:35: start model_add_line... INFO @ Fri, 26 Jun 2020 13:31:35: start X-correlation... INFO @ Fri, 26 Jun 2020 13:31:35: end of X-cor INFO @ Fri, 26 Jun 2020 13:31:35: #2 finished! INFO @ Fri, 26 Jun 2020 13:31:35: #2 predicted fragment length is 176 bps INFO @ Fri, 26 Jun 2020 13:31:35: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 26 Jun 2020 13:31:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.20_model.r WARNING @ Fri, 26 Jun 2020 13:31:35: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 13:31:35: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 26 Jun 2020 13:31:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 13:31:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 13:31:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 13:31:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 13:32:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.10_peaks.xls INFO @ Fri, 26 Jun 2020 13:32:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 13:32:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.10_summits.bed INFO @ Fri, 26 Jun 2020 13:32:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10961 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 13:32:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 13:32:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.20_peaks.xls INFO @ Fri, 26 Jun 2020 13:32:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 13:32:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1056724/SRX1056724.20_summits.bed INFO @ Fri, 26 Jun 2020 13:32:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7304 records, 4 fields): 9 millis CompletedMACS2peakCalling