Job ID = 6456816 SRX = SRX3981707 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:08:24 prefetch.2.10.7: 1) Downloading 'SRR7050523'... 2020-06-21T11:08:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:09:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:09:15 prefetch.2.10.7: 'SRR7050523' is valid 2020-06-21T11:09:15 prefetch.2.10.7: 1) 'SRR7050523' was downloaded successfully 2020-06-21T11:09:15 prefetch.2.10.7: 'SRR7050523' has 0 unresolved dependencies Read 7102119 spots for SRR7050523/SRR7050523.sra Written 7102119 spots for SRR7050523/SRR7050523.sra 2020-06-21T11:09:46 prefetch.2.10.7: 1) Downloading 'SRR7050524'... 2020-06-21T11:09:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:10:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:10:24 prefetch.2.10.7: 'SRR7050524' is valid 2020-06-21T11:10:24 prefetch.2.10.7: 1) 'SRR7050524' was downloaded successfully 2020-06-21T11:10:24 prefetch.2.10.7: 'SRR7050524' has 0 unresolved dependencies Read 7099332 spots for SRR7050524/SRR7050524.sra Written 7099332 spots for SRR7050524/SRR7050524.sra 2020-06-21T11:10:56 prefetch.2.10.7: 1) Downloading 'SRR7050525'... 2020-06-21T11:10:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:11:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:11:42 prefetch.2.10.7: 'SRR7050525' is valid 2020-06-21T11:11:42 prefetch.2.10.7: 1) 'SRR7050525' was downloaded successfully 2020-06-21T11:11:42 prefetch.2.10.7: 'SRR7050525' has 0 unresolved dependencies Read 7127665 spots for SRR7050525/SRR7050525.sra Written 7127665 spots for SRR7050525/SRR7050525.sra 2020-06-21T11:12:14 prefetch.2.10.7: 1) Downloading 'SRR7050526'... 2020-06-21T11:12:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:12:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:12:41 prefetch.2.10.7: 'SRR7050526' is valid 2020-06-21T11:12:41 prefetch.2.10.7: 1) 'SRR7050526' was downloaded successfully 2020-06-21T11:12:41 prefetch.2.10.7: 'SRR7050526' has 0 unresolved dependencies Read 7158814 spots for SRR7050526/SRR7050526.sra Written 7158814 spots for SRR7050526/SRR7050526.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: 00:07:07 28487930 reads; of these: 28487930 (100.00%) were unpaired; of these: 1037113 (3.64%) aligned 0 times 20782787 (72.95%) aligned exactly 1 time 6668030 (23.41%) aligned >1 times 96.36% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 4623835 / 27450817 = 0.1684 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 20:25:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.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 20:25:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:38: 1000000 INFO @ Sun, 21 Jun 2020 20:25:43: 2000000 INFO @ Sun, 21 Jun 2020 20:25:48: 3000000 INFO @ Sun, 21 Jun 2020 20:25:53: 4000000 INFO @ Sun, 21 Jun 2020 20:25:58: 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 20:26:03: 6000000 INFO @ Sun, 21 Jun 2020 20:26:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.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 20:26:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:08: 7000000 INFO @ Sun, 21 Jun 2020 20:26:09: 1000000 INFO @ Sun, 21 Jun 2020 20:26:14: 8000000 INFO @ Sun, 21 Jun 2020 20:26:14: 2000000 INFO @ Sun, 21 Jun 2020 20:26:19: 9000000 INFO @ Sun, 21 Jun 2020 20:26:19: 3000000 INFO @ Sun, 21 Jun 2020 20:26:24: 10000000 INFO @ Sun, 21 Jun 2020 20:26:25: 4000000 INFO @ Sun, 21 Jun 2020 20:26:29: 11000000 INFO @ Sun, 21 Jun 2020 20:26:30: 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 20:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.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 20:26:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:35: 12000000 INFO @ Sun, 21 Jun 2020 20:26:36: 6000000 INFO @ Sun, 21 Jun 2020 20:26:38: 1000000 INFO @ Sun, 21 Jun 2020 20:26:40: 13000000 INFO @ Sun, 21 Jun 2020 20:26:41: 7000000 INFO @ Sun, 21 Jun 2020 20:26:44: 2000000 INFO @ Sun, 21 Jun 2020 20:26:45: 14000000 INFO @ Sun, 21 Jun 2020 20:26:47: 8000000 INFO @ Sun, 21 Jun 2020 20:26:49: 3000000 INFO @ Sun, 21 Jun 2020 20:26:51: 15000000 INFO @ Sun, 21 Jun 2020 20:26:52: 9000000 INFO @ Sun, 21 Jun 2020 20:26:55: 4000000 INFO @ Sun, 21 Jun 2020 20:26:56: 16000000 INFO @ Sun, 21 Jun 2020 20:26:57: 10000000 INFO @ Sun, 21 Jun 2020 20:27:00: 5000000 INFO @ Sun, 21 Jun 2020 20:27:01: 17000000 INFO @ Sun, 21 Jun 2020 20:27:03: 11000000 INFO @ Sun, 21 Jun 2020 20:27:05: 6000000 INFO @ Sun, 21 Jun 2020 20:27:07: 18000000 INFO @ Sun, 21 Jun 2020 20:27:08: 12000000 INFO @ Sun, 21 Jun 2020 20:27:11: 7000000 INFO @ Sun, 21 Jun 2020 20:27:12: 19000000 INFO @ Sun, 21 Jun 2020 20:27:13: 13000000 INFO @ Sun, 21 Jun 2020 20:27:16: 8000000 INFO @ Sun, 21 Jun 2020 20:27:18: 20000000 INFO @ Sun, 21 Jun 2020 20:27:19: 14000000 INFO @ Sun, 21 Jun 2020 20:27:21: 9000000 INFO @ Sun, 21 Jun 2020 20:27:23: 21000000 INFO @ Sun, 21 Jun 2020 20:27:24: 15000000 INFO @ Sun, 21 Jun 2020 20:27:27: 10000000 INFO @ Sun, 21 Jun 2020 20:27:29: 22000000 INFO @ Sun, 21 Jun 2020 20:27:29: 16000000 INFO @ Sun, 21 Jun 2020 20:27:32: 11000000 INFO @ Sun, 21 Jun 2020 20:27:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:27:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:27:33: #1 total tags in treatment: 22826982 INFO @ Sun, 21 Jun 2020 20:27:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:33: #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 20:27:34: #1 tags after filtering in treatment: 22826914 INFO @ Sun, 21 Jun 2020 20:27:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:35: 17000000 INFO @ Sun, 21 Jun 2020 20:27:35: #2 number of paired peaks: 471 WARNING @ Sun, 21 Jun 2020 20:27:35: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Sun, 21 Jun 2020 20:27:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:36: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:27:36: #2 alternative fragment length(s) may be 2,52,582 bps INFO @ Sun, 21 Jun 2020 20:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.05_model.r WARNING @ Sun, 21 Jun 2020 20:27:36: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:27:36: #2 You may need to consider one of the other alternative d(s): 2,52,582 WARNING @ Sun, 21 Jun 2020 20:27:36: #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 20:27:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:37: 12000000 INFO @ Sun, 21 Jun 2020 20:27:40: 18000000 INFO @ Sun, 21 Jun 2020 20:27:42: 13000000 INFO @ Sun, 21 Jun 2020 20:27:45: 19000000 INFO @ Sun, 21 Jun 2020 20:27:48: 14000000 INFO @ Sun, 21 Jun 2020 20:27:51: 20000000 INFO @ Sun, 21 Jun 2020 20:27:53: 15000000 INFO @ Sun, 21 Jun 2020 20:27:57: 21000000 INFO @ Sun, 21 Jun 2020 20:27:58: 16000000 INFO @ Sun, 21 Jun 2020 20:28:02: 22000000 INFO @ Sun, 21 Jun 2020 20:28:03: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:28:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:07: #1 total tags in treatment: 22826982 INFO @ Sun, 21 Jun 2020 20:28:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:07: #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 20:28:08: #1 tags after filtering in treatment: 22826914 INFO @ Sun, 21 Jun 2020 20:28:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:08: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:09: 18000000 INFO @ Sun, 21 Jun 2020 20:28:09: #2 number of paired peaks: 471 WARNING @ Sun, 21 Jun 2020 20:28:09: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:09: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:09: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:09: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:09: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:09: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:28:09: #2 alternative fragment length(s) may be 2,52,582 bps INFO @ Sun, 21 Jun 2020 20:28:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.10_model.r WARNING @ Sun, 21 Jun 2020 20:28:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:28:09: #2 You may need to consider one of the other alternative d(s): 2,52,582 WARNING @ Sun, 21 Jun 2020 20:28:09: #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 20:28:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:14: 19000000 INFO @ Sun, 21 Jun 2020 20:28:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:28:19: 20000000 INFO @ Sun, 21 Jun 2020 20:28:24: 21000000 INFO @ Sun, 21 Jun 2020 20:28:29: 22000000 INFO @ Sun, 21 Jun 2020 20:28:34: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:28:34: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:28:34: #1 total tags in treatment: 22826982 INFO @ Sun, 21 Jun 2020 20:28:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:34: #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 20:28:34: #1 tags after filtering in treatment: 22826914 INFO @ Sun, 21 Jun 2020 20:28:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:36: #2 number of paired peaks: 471 WARNING @ Sun, 21 Jun 2020 20:28:36: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Sun, 21 Jun 2020 20:28:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:36: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:28:36: #2 alternative fragment length(s) may be 2,52,582 bps INFO @ Sun, 21 Jun 2020 20:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.20_model.r WARNING @ Sun, 21 Jun 2020 20:28:36: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:28:36: #2 You may need to consider one of the other alternative d(s): 2,52,582 WARNING @ Sun, 21 Jun 2020 20:28:36: #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 20:28:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.05_summits.bed INFO @ Sun, 21 Jun 2020 20:28:37: Done! pass1 - making usageList (636 chroms): 1 millis pass2 - checking and writing primary data (3706 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:28:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.10_summits.bed INFO @ Sun, 21 Jun 2020 20:29:14: Done! pass1 - making usageList (418 chroms): 1 millis pass2 - checking and writing primary data (1458 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:29:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981707/SRX3981707.20_summits.bed INFO @ Sun, 21 Jun 2020 20:29:37: Done! pass1 - making usageList (178 chroms): 0 millis pass2 - checking and writing primary data (520 records, 4 fields): 6 millis CompletedMACS2peakCalling