Job ID = 6453198 SRX = SRX1078887 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:11:18 prefetch.2.10.7: 1) Downloading 'SRR2084572'... 2020-06-21T08:11:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:12:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:12:00 prefetch.2.10.7: 'SRR2084572' is valid 2020-06-21T08:12:00 prefetch.2.10.7: 1) 'SRR2084572' was downloaded successfully 2020-06-21T08:12:00 prefetch.2.10.7: 'SRR2084572' has 0 unresolved dependencies Read 5566758 spots for SRR2084572/SRR2084572.sra Written 5566758 spots for SRR2084572/SRR2084572.sra 2020-06-21T08:12:30 prefetch.2.10.7: 1) Downloading 'SRR2084573'... 2020-06-21T08:12:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:14:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:14:05 prefetch.2.10.7: 'SRR2084573' is valid 2020-06-21T08:14:05 prefetch.2.10.7: 1) 'SRR2084573' was downloaded successfully 2020-06-21T08:14:05 prefetch.2.10.7: 'SRR2084573' has 0 unresolved dependencies Read 5507098 spots for SRR2084573/SRR2084573.sra Written 5507098 spots for SRR2084573/SRR2084573.sra 2020-06-21T08:14:35 prefetch.2.10.7: 1) Downloading 'SRR2084574'... 2020-06-21T08:14:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:15:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:15:22 prefetch.2.10.7: 'SRR2084574' is valid 2020-06-21T08:15:22 prefetch.2.10.7: 1) 'SRR2084574' was downloaded successfully 2020-06-21T08:15:22 prefetch.2.10.7: 'SRR2084574' has 0 unresolved dependencies Read 5450510 spots for SRR2084574/SRR2084574.sra Written 5450510 spots for SRR2084574/SRR2084574.sra 2020-06-21T08:15:51 prefetch.2.10.7: 1) Downloading 'SRR2084575'... 2020-06-21T08:15:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:16:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:16:41 prefetch.2.10.7: 'SRR2084575' is valid 2020-06-21T08:16:41 prefetch.2.10.7: 1) 'SRR2084575' was downloaded successfully 2020-06-21T08:16:41 prefetch.2.10.7: 'SRR2084575' has 0 unresolved dependencies Read 5362760 spots for SRR2084575/SRR2084575.sra Written 5362760 spots for SRR2084575/SRR2084575.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: 00:06:05 21887126 reads; of these: 21887126 (100.00%) were unpaired; of these: 2091970 (9.56%) aligned 0 times 13511605 (61.73%) aligned exactly 1 time 6283551 (28.71%) aligned >1 times 90.44% overall alignment rate Time searching: 00:06:05 Overall time: 00:06:05 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 12 files... [bam_rmdupse_core] 3049850 / 19795156 = 0.1541 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 17:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.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 17:28:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:41: 1000000 INFO @ Sun, 21 Jun 2020 17:28:47: 2000000 INFO @ Sun, 21 Jun 2020 17:28:53: 3000000 INFO @ Sun, 21 Jun 2020 17:29:00: 4000000 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 17:29:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.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 17:29:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:06: 5000000 INFO @ Sun, 21 Jun 2020 17:29:12: 1000000 INFO @ Sun, 21 Jun 2020 17:29:13: 6000000 INFO @ Sun, 21 Jun 2020 17:29:19: 2000000 INFO @ Sun, 21 Jun 2020 17:29:19: 7000000 INFO @ Sun, 21 Jun 2020 17:29:26: 3000000 INFO @ Sun, 21 Jun 2020 17:29:26: 8000000 INFO @ Sun, 21 Jun 2020 17:29:32: 4000000 INFO @ Sun, 21 Jun 2020 17:29:33: 9000000 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 17:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.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 17:29:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:39: 10000000 INFO @ Sun, 21 Jun 2020 17:29:39: 5000000 INFO @ Sun, 21 Jun 2020 17:29:42: 1000000 INFO @ Sun, 21 Jun 2020 17:29:46: 11000000 INFO @ Sun, 21 Jun 2020 17:29:47: 6000000 INFO @ Sun, 21 Jun 2020 17:29:48: 2000000 INFO @ Sun, 21 Jun 2020 17:29:53: 12000000 INFO @ Sun, 21 Jun 2020 17:29:54: 7000000 INFO @ Sun, 21 Jun 2020 17:29:54: 3000000 INFO @ Sun, 21 Jun 2020 17:30:00: 13000000 INFO @ Sun, 21 Jun 2020 17:30:00: 4000000 INFO @ Sun, 21 Jun 2020 17:30:01: 8000000 INFO @ Sun, 21 Jun 2020 17:30:07: 5000000 INFO @ Sun, 21 Jun 2020 17:30:07: 14000000 INFO @ Sun, 21 Jun 2020 17:30:08: 9000000 INFO @ Sun, 21 Jun 2020 17:30:13: 6000000 INFO @ Sun, 21 Jun 2020 17:30:14: 15000000 INFO @ Sun, 21 Jun 2020 17:30:16: 10000000 INFO @ Sun, 21 Jun 2020 17:30:19: 7000000 INFO @ Sun, 21 Jun 2020 17:30:21: 16000000 INFO @ Sun, 21 Jun 2020 17:30:23: 11000000 INFO @ Sun, 21 Jun 2020 17:30:26: 8000000 INFO @ Sun, 21 Jun 2020 17:30:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:30:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:30:26: #1 total tags in treatment: 16745306 INFO @ Sun, 21 Jun 2020 17:30:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:26: #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 17:30:26: #1 tags after filtering in treatment: 16745233 INFO @ Sun, 21 Jun 2020 17:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:28: #2 number of paired peaks: 1521 INFO @ Sun, 21 Jun 2020 17:30:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:28: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 17:30:28: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 17:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.05_model.r WARNING @ Sun, 21 Jun 2020 17:30:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:30:28: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 17:30:28: #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 17:30:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:30: 12000000 INFO @ Sun, 21 Jun 2020 17:30:32: 9000000 INFO @ Sun, 21 Jun 2020 17:30:37: 13000000 INFO @ Sun, 21 Jun 2020 17:30:38: 10000000 INFO @ Sun, 21 Jun 2020 17:30:45: 11000000 INFO @ Sun, 21 Jun 2020 17:30:45: 14000000 INFO @ Sun, 21 Jun 2020 17:30:51: 12000000 INFO @ Sun, 21 Jun 2020 17:30:52: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:30:57: 13000000 INFO @ Sun, 21 Jun 2020 17:30:59: 16000000 INFO @ Sun, 21 Jun 2020 17:31:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:04: 14000000 INFO @ Sun, 21 Jun 2020 17:31:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:31:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:31:05: #1 total tags in treatment: 16745306 INFO @ Sun, 21 Jun 2020 17:31:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:05: #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 17:31:05: #1 tags after filtering in treatment: 16745233 INFO @ Sun, 21 Jun 2020 17:31:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:06: #2 number of paired peaks: 1521 INFO @ Sun, 21 Jun 2020 17:31:06: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:06: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:06: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:06: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:06: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 17:31:06: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 17:31:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.10_model.r WARNING @ Sun, 21 Jun 2020 17:31:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:06: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 17:31:06: #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 17:31:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:09: 15000000 INFO @ Sun, 21 Jun 2020 17:31:15: 16000000 INFO @ Sun, 21 Jun 2020 17:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.05_summits.bed INFO @ Sun, 21 Jun 2020 17:31:17: Done! pass1 - making usageList (634 chroms): 1 millis pass2 - checking and writing primary data (2944 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:31:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:31:20: #1 total tags in treatment: 16745306 INFO @ Sun, 21 Jun 2020 17:31:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:20: #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 17:31:20: #1 tags after filtering in treatment: 16745233 INFO @ Sun, 21 Jun 2020 17:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:20: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:21: #2 number of paired peaks: 1521 INFO @ Sun, 21 Jun 2020 17:31:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:22: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 17:31:22: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 17:31:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.20_model.r WARNING @ Sun, 21 Jun 2020 17:31:22: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:31:22: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 17:31:22: #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 17:31:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:31:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.10_summits.bed INFO @ Sun, 21 Jun 2020 17:31:55: Done! pass1 - making usageList (545 chroms): 1 millis pass2 - checking and writing primary data (2221 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1078887/SRX1078887.20_summits.bed INFO @ Sun, 21 Jun 2020 17:32:11: Done! pass1 - making usageList (447 chroms): 1 millis pass2 - checking and writing primary data (1368 records, 4 fields): 14 millis CompletedMACS2peakCalling