Job ID = 6453236 SRX = SRX110758 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:15:18 prefetch.2.10.7: 1) Downloading 'SRR388340'... 2020-06-21T08:15:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:19:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:19:37 prefetch.2.10.7: 1) 'SRR388340' was downloaded successfully Read 36336395 spots for SRR388340/SRR388340.sra Written 36336395 spots for SRR388340/SRR388340.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: 00:06:24 36336395 reads; of these: 36336395 (100.00%) were unpaired; of these: 5384026 (14.82%) aligned 0 times 26599948 (73.20%) aligned exactly 1 time 4352421 (11.98%) aligned >1 times 85.18% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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 8 files... [bam_rmdupse_core] 12198086 / 30952369 = 0.3941 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 17:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.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 17:33:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:33:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:33:42: 1000000 INFO @ Sun, 21 Jun 2020 17:33:47: 2000000 INFO @ Sun, 21 Jun 2020 17:33:53: 3000000 INFO @ Sun, 21 Jun 2020 17:33:58: 4000000 INFO @ Sun, 21 Jun 2020 17:34:04: 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 17:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.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 17:34:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:09: 6000000 INFO @ Sun, 21 Jun 2020 17:34:12: 1000000 INFO @ Sun, 21 Jun 2020 17:34:15: 7000000 INFO @ Sun, 21 Jun 2020 17:34:17: 2000000 INFO @ Sun, 21 Jun 2020 17:34:21: 8000000 INFO @ Sun, 21 Jun 2020 17:34:22: 3000000 INFO @ Sun, 21 Jun 2020 17:34:26: 9000000 INFO @ Sun, 21 Jun 2020 17:34:27: 4000000 INFO @ Sun, 21 Jun 2020 17:34:32: 10000000 INFO @ Sun, 21 Jun 2020 17:34:32: 5000000 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 17:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.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 17:34:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:34:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:34:38: 6000000 INFO @ Sun, 21 Jun 2020 17:34:38: 11000000 INFO @ Sun, 21 Jun 2020 17:34:42: 1000000 INFO @ Sun, 21 Jun 2020 17:34:43: 7000000 INFO @ Sun, 21 Jun 2020 17:34:44: 12000000 INFO @ Sun, 21 Jun 2020 17:34:47: 2000000 INFO @ Sun, 21 Jun 2020 17:34:48: 8000000 INFO @ Sun, 21 Jun 2020 17:34:49: 13000000 INFO @ Sun, 21 Jun 2020 17:34:52: 3000000 INFO @ Sun, 21 Jun 2020 17:34:54: 9000000 INFO @ Sun, 21 Jun 2020 17:34:55: 14000000 INFO @ Sun, 21 Jun 2020 17:34:57: 4000000 INFO @ Sun, 21 Jun 2020 17:34:59: 10000000 INFO @ Sun, 21 Jun 2020 17:35:01: 15000000 INFO @ Sun, 21 Jun 2020 17:35:03: 5000000 INFO @ Sun, 21 Jun 2020 17:35:04: 11000000 INFO @ Sun, 21 Jun 2020 17:35:07: 16000000 INFO @ Sun, 21 Jun 2020 17:35:08: 6000000 INFO @ Sun, 21 Jun 2020 17:35:09: 12000000 INFO @ Sun, 21 Jun 2020 17:35:13: 17000000 INFO @ Sun, 21 Jun 2020 17:35:13: 7000000 INFO @ Sun, 21 Jun 2020 17:35:14: 13000000 INFO @ Sun, 21 Jun 2020 17:35:18: 8000000 INFO @ Sun, 21 Jun 2020 17:35:19: 18000000 INFO @ Sun, 21 Jun 2020 17:35:20: 14000000 INFO @ Sun, 21 Jun 2020 17:35:23: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:35:23: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:35:23: #1 total tags in treatment: 18754283 INFO @ Sun, 21 Jun 2020 17:35:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:23: #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 17:35:24: 9000000 INFO @ Sun, 21 Jun 2020 17:35:24: #1 tags after filtering in treatment: 18754251 INFO @ Sun, 21 Jun 2020 17:35:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:25: 15000000 INFO @ Sun, 21 Jun 2020 17:35:26: #2 number of paired peaks: 4345 INFO @ Sun, 21 Jun 2020 17:35:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:26: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 17:35:26: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 17:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.05_model.r WARNING @ Sun, 21 Jun 2020 17:35:26: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:35:26: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 17:35:26: #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 17:35:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:35:29: 10000000 INFO @ Sun, 21 Jun 2020 17:35:30: 16000000 INFO @ Sun, 21 Jun 2020 17:35:34: 11000000 INFO @ Sun, 21 Jun 2020 17:35:35: 17000000 INFO @ Sun, 21 Jun 2020 17:35:39: 12000000 INFO @ Sun, 21 Jun 2020 17:35:40: 18000000 INFO @ Sun, 21 Jun 2020 17:35:44: 13000000 INFO @ Sun, 21 Jun 2020 17:35:45: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:35:45: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:35:45: #1 total tags in treatment: 18754283 INFO @ Sun, 21 Jun 2020 17:35:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:35:45: #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 17:35:45: #1 tags after filtering in treatment: 18754251 INFO @ Sun, 21 Jun 2020 17:35:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:35:45: #1 finished! INFO @ Sun, 21 Jun 2020 17:35:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:35:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:35:47: #2 number of paired peaks: 4345 INFO @ Sun, 21 Jun 2020 17:35:47: start model_add_line... INFO @ Sun, 21 Jun 2020 17:35:47: start X-correlation... INFO @ Sun, 21 Jun 2020 17:35:47: end of X-cor INFO @ Sun, 21 Jun 2020 17:35:47: #2 finished! INFO @ Sun, 21 Jun 2020 17:35:47: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 17:35:47: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 17:35:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.10_model.r WARNING @ Sun, 21 Jun 2020 17:35:47: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:35:47: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 17:35:47: #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 17:35:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:35:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:35:49: 14000000 INFO @ Sun, 21 Jun 2020 17:35:53: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:35:58: 16000000 INFO @ Sun, 21 Jun 2020 17:36:03: 17000000 INFO @ Sun, 21 Jun 2020 17:36:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:36:08: 18000000 INFO @ Sun, 21 Jun 2020 17:36:12: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:36:12: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:36:12: #1 total tags in treatment: 18754283 INFO @ Sun, 21 Jun 2020 17:36:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:36:12: #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 17:36:12: #1 tags after filtering in treatment: 18754251 INFO @ Sun, 21 Jun 2020 17:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:36:12: #1 finished! INFO @ Sun, 21 Jun 2020 17:36:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:36:14: #2 number of paired peaks: 4345 INFO @ Sun, 21 Jun 2020 17:36:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:36:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:36:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:36:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:36:14: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 17:36:14: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 17:36:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.20_model.r WARNING @ Sun, 21 Jun 2020 17:36:14: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:36:14: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 17:36:14: #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 17:36:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:36:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:36:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:36:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:36:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.05_summits.bed INFO @ Sun, 21 Jun 2020 17:36:26: Done! INFO @ Sun, 21 Jun 2020 17:36:26: #3 Call peaks for each chromosome... pass1 - making usageList (171 chroms): 3 millis pass2 - checking and writing primary data (18828 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.10_summits.bed INFO @ Sun, 21 Jun 2020 17:36:47: Done! pass1 - making usageList (128 chroms): 2 millis pass2 - checking and writing primary data (13162 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:36:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:37:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:37:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:37:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110758/SRX110758.20_summits.bed INFO @ Sun, 21 Jun 2020 17:37:13: Done! pass1 - making usageList (85 chroms): 2 millis pass2 - checking and writing primary data (7733 records, 4 fields): 9 millis CompletedMACS2peakCalling