Job ID = 6456815 SRX = SRX3981706 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:19:39 prefetch.2.10.7: 1) Downloading 'SRR7050519'... 2020-06-21T11:19:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:20:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:20:46 prefetch.2.10.7: 'SRR7050519' is valid 2020-06-21T11:20:46 prefetch.2.10.7: 1) 'SRR7050519' was downloaded successfully 2020-06-21T11:20:46 prefetch.2.10.7: 'SRR7050519' has 0 unresolved dependencies Read 7873433 spots for SRR7050519/SRR7050519.sra Written 7873433 spots for SRR7050519/SRR7050519.sra 2020-06-21T11:21:20 prefetch.2.10.7: 1) Downloading 'SRR7050520'... 2020-06-21T11:21:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:44 prefetch.2.10.7: 'SRR7050520' is valid 2020-06-21T11:22:44 prefetch.2.10.7: 1) 'SRR7050520' was downloaded successfully 2020-06-21T11:22:44 prefetch.2.10.7: 'SRR7050520' has 0 unresolved dependencies Read 7862744 spots for SRR7050520/SRR7050520.sra Written 7862744 spots for SRR7050520/SRR7050520.sra 2020-06-21T11:23:19 prefetch.2.10.7: 1) Downloading 'SRR7050521'... 2020-06-21T11:23:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:13 prefetch.2.10.7: 'SRR7050521' is valid 2020-06-21T11:24:13 prefetch.2.10.7: 1) 'SRR7050521' was downloaded successfully 2020-06-21T11:24:13 prefetch.2.10.7: 'SRR7050521' has 0 unresolved dependencies Read 7895584 spots for SRR7050521/SRR7050521.sra Written 7895584 spots for SRR7050521/SRR7050521.sra 2020-06-21T11:24:48 prefetch.2.10.7: 1) Downloading 'SRR7050522'... 2020-06-21T11:24:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:26:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:26:09 prefetch.2.10.7: 'SRR7050522' is valid 2020-06-21T11:26:09 prefetch.2.10.7: 1) 'SRR7050522' was downloaded successfully 2020-06-21T11:26:09 prefetch.2.10.7: 'SRR7050522' has 0 unresolved dependencies Read 7931868 spots for SRR7050522/SRR7050522.sra Written 7931868 spots for SRR7050522/SRR7050522.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: 00:07:38 31563629 reads; of these: 31563629 (100.00%) were unpaired; of these: 1475581 (4.67%) aligned 0 times 23463532 (74.34%) aligned exactly 1 time 6624516 (20.99%) aligned >1 times 95.33% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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 16 files... [bam_rmdupse_core] 4529640 / 30088048 = 0.1505 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 20:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.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 20:40:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:22: 1000000 INFO @ Sun, 21 Jun 2020 20:40:27: 2000000 INFO @ Sun, 21 Jun 2020 20:40:32: 3000000 INFO @ Sun, 21 Jun 2020 20:40:36: 4000000 INFO @ Sun, 21 Jun 2020 20:40:41: 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 20:40:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.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 20:40:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:46: 6000000 INFO @ Sun, 21 Jun 2020 20:40:49: 1000000 INFO @ Sun, 21 Jun 2020 20:40:50: 7000000 INFO @ Sun, 21 Jun 2020 20:40:54: 2000000 INFO @ Sun, 21 Jun 2020 20:40:55: 8000000 INFO @ Sun, 21 Jun 2020 20:40:59: 3000000 INFO @ Sun, 21 Jun 2020 20:41:00: 9000000 INFO @ Sun, 21 Jun 2020 20:41:04: 4000000 INFO @ Sun, 21 Jun 2020 20:41:05: 10000000 INFO @ Sun, 21 Jun 2020 20:41:08: 5000000 INFO @ Sun, 21 Jun 2020 20:41:09: 11000000 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 20:41:13: 6000000 INFO @ Sun, 21 Jun 2020 20:41:14: 12000000 INFO @ Sun, 21 Jun 2020 20:41:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.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 20:41:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:41:18: 7000000 INFO @ Sun, 21 Jun 2020 20:41:19: 13000000 INFO @ Sun, 21 Jun 2020 20:41:20: 1000000 INFO @ Sun, 21 Jun 2020 20:41:23: 8000000 INFO @ Sun, 21 Jun 2020 20:41:24: 14000000 INFO @ Sun, 21 Jun 2020 20:41:25: 2000000 INFO @ Sun, 21 Jun 2020 20:41:28: 9000000 INFO @ Sun, 21 Jun 2020 20:41:29: 15000000 INFO @ Sun, 21 Jun 2020 20:41:30: 3000000 INFO @ Sun, 21 Jun 2020 20:41:32: 10000000 INFO @ Sun, 21 Jun 2020 20:41:34: 16000000 INFO @ Sun, 21 Jun 2020 20:41:35: 4000000 INFO @ Sun, 21 Jun 2020 20:41:37: 11000000 INFO @ Sun, 21 Jun 2020 20:41:39: 17000000 INFO @ Sun, 21 Jun 2020 20:41:40: 5000000 INFO @ Sun, 21 Jun 2020 20:41:42: 12000000 INFO @ Sun, 21 Jun 2020 20:41:43: 18000000 INFO @ Sun, 21 Jun 2020 20:41:45: 6000000 INFO @ Sun, 21 Jun 2020 20:41:47: 13000000 INFO @ Sun, 21 Jun 2020 20:41:48: 19000000 INFO @ Sun, 21 Jun 2020 20:41:50: 7000000 INFO @ Sun, 21 Jun 2020 20:41:51: 14000000 INFO @ Sun, 21 Jun 2020 20:41:53: 20000000 INFO @ Sun, 21 Jun 2020 20:41:55: 8000000 INFO @ Sun, 21 Jun 2020 20:41:56: 15000000 INFO @ Sun, 21 Jun 2020 20:41:58: 21000000 INFO @ Sun, 21 Jun 2020 20:42:00: 9000000 INFO @ Sun, 21 Jun 2020 20:42:01: 16000000 INFO @ Sun, 21 Jun 2020 20:42:03: 22000000 INFO @ Sun, 21 Jun 2020 20:42:05: 10000000 INFO @ Sun, 21 Jun 2020 20:42:06: 17000000 INFO @ Sun, 21 Jun 2020 20:42:08: 23000000 INFO @ Sun, 21 Jun 2020 20:42:10: 11000000 INFO @ Sun, 21 Jun 2020 20:42:11: 18000000 INFO @ Sun, 21 Jun 2020 20:42:13: 24000000 INFO @ Sun, 21 Jun 2020 20:42:15: 12000000 INFO @ Sun, 21 Jun 2020 20:42:15: 19000000 INFO @ Sun, 21 Jun 2020 20:42:19: 25000000 INFO @ Sun, 21 Jun 2020 20:42:20: 20000000 INFO @ Sun, 21 Jun 2020 20:42:21: 13000000 INFO @ Sun, 21 Jun 2020 20:42:22: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:22: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:22: #1 total tags in treatment: 25558408 INFO @ Sun, 21 Jun 2020 20:42:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:22: #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 20:42:22: #1 tags after filtering in treatment: 25558350 INFO @ Sun, 21 Jun 2020 20:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:22: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:24: #2 number of paired peaks: 412 WARNING @ Sun, 21 Jun 2020 20:42:24: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 21 Jun 2020 20:42:24: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:24: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 20:42:24: #2 alternative fragment length(s) may be 3,84,598 bps INFO @ Sun, 21 Jun 2020 20:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.05_model.r WARNING @ Sun, 21 Jun 2020 20:42:24: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:42:24: #2 You may need to consider one of the other alternative d(s): 3,84,598 WARNING @ Sun, 21 Jun 2020 20:42:24: #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 20:42:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:25: 21000000 INFO @ Sun, 21 Jun 2020 20:42:26: 14000000 INFO @ Sun, 21 Jun 2020 20:42:30: 22000000 INFO @ Sun, 21 Jun 2020 20:42:31: 15000000 INFO @ Sun, 21 Jun 2020 20:42:35: 23000000 INFO @ Sun, 21 Jun 2020 20:42:37: 16000000 INFO @ Sun, 21 Jun 2020 20:42:40: 24000000 INFO @ Sun, 21 Jun 2020 20:42:42: 17000000 INFO @ Sun, 21 Jun 2020 20:42:45: 25000000 INFO @ Sun, 21 Jun 2020 20:42:48: 18000000 INFO @ Sun, 21 Jun 2020 20:42:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:48: #1 total tags in treatment: 25558408 INFO @ Sun, 21 Jun 2020 20:42:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:48: #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 20:42:49: #1 tags after filtering in treatment: 25558350 INFO @ Sun, 21 Jun 2020 20:42:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:51: #2 number of paired peaks: 412 WARNING @ Sun, 21 Jun 2020 20:42:51: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 21 Jun 2020 20:42:51: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:51: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:51: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:51: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:51: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 20:42:51: #2 alternative fragment length(s) may be 3,84,598 bps INFO @ Sun, 21 Jun 2020 20:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.10_model.r WARNING @ Sun, 21 Jun 2020 20:42:51: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:42:51: #2 You may need to consider one of the other alternative d(s): 3,84,598 WARNING @ Sun, 21 Jun 2020 20:42:51: #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 20:42:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:42:53: 19000000 INFO @ Sun, 21 Jun 2020 20:42:59: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:43:04: 21000000 INFO @ Sun, 21 Jun 2020 20:43:10: 22000000 INFO @ Sun, 21 Jun 2020 20:43:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:15: 23000000 INFO @ Sun, 21 Jun 2020 20:43:21: 24000000 INFO @ Sun, 21 Jun 2020 20:43:26: 25000000 INFO @ Sun, 21 Jun 2020 20:43:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:30: #1 total tags in treatment: 25558408 INFO @ Sun, 21 Jun 2020 20:43:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:30: #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 20:43:30: #1 tags after filtering in treatment: 25558350 INFO @ Sun, 21 Jun 2020 20:43:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:32: #2 number of paired peaks: 412 WARNING @ Sun, 21 Jun 2020 20:43:32: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Sun, 21 Jun 2020 20:43:32: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:32: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:32: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:32: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:32: #2 predicted fragment length is 84 bps INFO @ Sun, 21 Jun 2020 20:43:32: #2 alternative fragment length(s) may be 3,84,598 bps INFO @ Sun, 21 Jun 2020 20:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.20_model.r WARNING @ Sun, 21 Jun 2020 20:43:32: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:43:32: #2 You may need to consider one of the other alternative d(s): 3,84,598 WARNING @ Sun, 21 Jun 2020 20:43:32: #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 20:43:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.05_summits.bed INFO @ Sun, 21 Jun 2020 20:43:35: Done! pass1 - making usageList (592 chroms): 2 millis pass2 - checking and writing primary data (4605 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.10_summits.bed INFO @ Sun, 21 Jun 2020 20:44:02: Done! pass1 - making usageList (329 chroms): 1 millis pass2 - checking and writing primary data (1831 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981706/SRX3981706.20_summits.bed INFO @ Sun, 21 Jun 2020 20:44:42: Done! pass1 - making usageList (157 chroms): 1 millis pass2 - checking and writing primary data (615 records, 4 fields): 6 millis CompletedMACS2peakCalling