Job ID = 6456821 SRX = SRX3981709 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:07:39 prefetch.2.10.7: 1) Downloading 'SRR7050531'... 2020-06-21T11:07:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:08:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:08:38 prefetch.2.10.7: 'SRR7050531' is valid 2020-06-21T11:08:38 prefetch.2.10.7: 1) 'SRR7050531' was downloaded successfully 2020-06-21T11:08:38 prefetch.2.10.7: 'SRR7050531' has 0 unresolved dependencies Read 8581094 spots for SRR7050531/SRR7050531.sra Written 8581094 spots for SRR7050531/SRR7050531.sra 2020-06-21T11:09:13 prefetch.2.10.7: 1) Downloading 'SRR7050532'... 2020-06-21T11:09:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:10:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:10:18 prefetch.2.10.7: 'SRR7050532' is valid 2020-06-21T11:10:18 prefetch.2.10.7: 1) 'SRR7050532' was downloaded successfully 2020-06-21T11:10:18 prefetch.2.10.7: 'SRR7050532' has 0 unresolved dependencies Read 8577033 spots for SRR7050532/SRR7050532.sra Written 8577033 spots for SRR7050532/SRR7050532.sra 2020-06-21T11:10:54 prefetch.2.10.7: 1) Downloading 'SRR7050533'... 2020-06-21T11:10:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:11:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:11:59 prefetch.2.10.7: 'SRR7050533' is valid 2020-06-21T11:11:59 prefetch.2.10.7: 1) 'SRR7050533' was downloaded successfully 2020-06-21T11:11:59 prefetch.2.10.7: 'SRR7050533' has 0 unresolved dependencies Read 8610938 spots for SRR7050533/SRR7050533.sra Written 8610938 spots for SRR7050533/SRR7050533.sra 2020-06-21T11:12:35 prefetch.2.10.7: 1) Downloading 'SRR7050534'... 2020-06-21T11:12:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:13:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:13:45 prefetch.2.10.7: 'SRR7050534' is valid 2020-06-21T11:13:45 prefetch.2.10.7: 1) 'SRR7050534' was downloaded successfully 2020-06-21T11:13:45 prefetch.2.10.7: 'SRR7050534' has 0 unresolved dependencies Read 8649782 spots for SRR7050534/SRR7050534.sra Written 8649782 spots for SRR7050534/SRR7050534.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: 00:08:53 34418847 reads; of these: 34418847 (100.00%) were unpaired; of these: 1416253 (4.11%) aligned 0 times 24672684 (71.68%) aligned exactly 1 time 8329910 (24.20%) aligned >1 times 95.89% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 5353286 / 33002594 = 0.1622 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 20:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.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 20:29:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:29: 1000000 INFO @ Sun, 21 Jun 2020 20:29:34: 2000000 INFO @ Sun, 21 Jun 2020 20:29:39: 3000000 INFO @ Sun, 21 Jun 2020 20:29:43: 4000000 INFO @ Sun, 21 Jun 2020 20:29:48: 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 20:29:53: 6000000 INFO @ Sun, 21 Jun 2020 20:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.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 20:29:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:29:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:29:57: 7000000 INFO @ Sun, 21 Jun 2020 20:29:59: 1000000 INFO @ Sun, 21 Jun 2020 20:30:02: 8000000 INFO @ Sun, 21 Jun 2020 20:30:04: 2000000 INFO @ Sun, 21 Jun 2020 20:30:07: 9000000 INFO @ Sun, 21 Jun 2020 20:30:09: 3000000 INFO @ Sun, 21 Jun 2020 20:30:12: 10000000 INFO @ Sun, 21 Jun 2020 20:30:14: 4000000 INFO @ Sun, 21 Jun 2020 20:30:17: 11000000 INFO @ Sun, 21 Jun 2020 20:30:19: 5000000 INFO @ Sun, 21 Jun 2020 20:30:21: 12000000 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 20:30:24: 6000000 INFO @ Sun, 21 Jun 2020 20:30:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.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 20:30:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:26: 13000000 INFO @ Sun, 21 Jun 2020 20:30:29: 7000000 INFO @ Sun, 21 Jun 2020 20:30:29: 1000000 INFO @ Sun, 21 Jun 2020 20:30:31: 14000000 INFO @ Sun, 21 Jun 2020 20:30:33: 8000000 INFO @ Sun, 21 Jun 2020 20:30:34: 2000000 INFO @ Sun, 21 Jun 2020 20:30:36: 15000000 INFO @ Sun, 21 Jun 2020 20:30:38: 9000000 INFO @ Sun, 21 Jun 2020 20:30:39: 3000000 INFO @ Sun, 21 Jun 2020 20:30:41: 16000000 INFO @ Sun, 21 Jun 2020 20:30:43: 10000000 INFO @ Sun, 21 Jun 2020 20:30:44: 4000000 INFO @ Sun, 21 Jun 2020 20:30:46: 17000000 INFO @ Sun, 21 Jun 2020 20:30:48: 11000000 INFO @ Sun, 21 Jun 2020 20:30:49: 5000000 INFO @ Sun, 21 Jun 2020 20:30:51: 18000000 INFO @ Sun, 21 Jun 2020 20:30:53: 12000000 INFO @ Sun, 21 Jun 2020 20:30:54: 6000000 INFO @ Sun, 21 Jun 2020 20:30:55: 19000000 INFO @ Sun, 21 Jun 2020 20:30:58: 13000000 INFO @ Sun, 21 Jun 2020 20:30:59: 7000000 INFO @ Sun, 21 Jun 2020 20:31:00: 20000000 INFO @ Sun, 21 Jun 2020 20:31:02: 14000000 INFO @ Sun, 21 Jun 2020 20:31:04: 8000000 INFO @ Sun, 21 Jun 2020 20:31:05: 21000000 INFO @ Sun, 21 Jun 2020 20:31:07: 15000000 INFO @ Sun, 21 Jun 2020 20:31:09: 9000000 INFO @ Sun, 21 Jun 2020 20:31:10: 22000000 INFO @ Sun, 21 Jun 2020 20:31:12: 16000000 INFO @ Sun, 21 Jun 2020 20:31:14: 10000000 INFO @ Sun, 21 Jun 2020 20:31:15: 23000000 INFO @ Sun, 21 Jun 2020 20:31:17: 17000000 INFO @ Sun, 21 Jun 2020 20:31:19: 11000000 INFO @ Sun, 21 Jun 2020 20:31:20: 24000000 INFO @ Sun, 21 Jun 2020 20:31:22: 18000000 INFO @ Sun, 21 Jun 2020 20:31:24: 12000000 INFO @ Sun, 21 Jun 2020 20:31:25: 25000000 INFO @ Sun, 21 Jun 2020 20:31:27: 19000000 INFO @ Sun, 21 Jun 2020 20:31:29: 13000000 INFO @ Sun, 21 Jun 2020 20:31:30: 26000000 INFO @ Sun, 21 Jun 2020 20:31:32: 20000000 INFO @ Sun, 21 Jun 2020 20:31:33: 14000000 INFO @ Sun, 21 Jun 2020 20:31:35: 27000000 INFO @ Sun, 21 Jun 2020 20:31:36: 21000000 INFO @ Sun, 21 Jun 2020 20:31:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:38: #1 total tags in treatment: 27649308 INFO @ Sun, 21 Jun 2020 20:31:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:38: #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 20:31:38: 15000000 INFO @ Sun, 21 Jun 2020 20:31:39: #1 tags after filtering in treatment: 27649261 INFO @ Sun, 21 Jun 2020 20:31:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:41: #2 number of paired peaks: 356 WARNING @ Sun, 21 Jun 2020 20:31:41: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sun, 21 Jun 2020 20:31:41: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:41: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:41: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:41: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:41: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:31:41: #2 alternative fragment length(s) may be 1,50 bps INFO @ Sun, 21 Jun 2020 20:31:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.05_model.r WARNING @ Sun, 21 Jun 2020 20:31:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:31:41: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Sun, 21 Jun 2020 20:31:41: #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 20:31:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:31:41: 22000000 INFO @ Sun, 21 Jun 2020 20:31:43: 16000000 INFO @ Sun, 21 Jun 2020 20:31:46: 23000000 INFO @ Sun, 21 Jun 2020 20:31:48: 17000000 INFO @ Sun, 21 Jun 2020 20:31:51: 24000000 INFO @ Sun, 21 Jun 2020 20:31:53: 18000000 INFO @ Sun, 21 Jun 2020 20:31:56: 25000000 INFO @ Sun, 21 Jun 2020 20:31:58: 19000000 INFO @ Sun, 21 Jun 2020 20:32:01: 26000000 INFO @ Sun, 21 Jun 2020 20:32:03: 20000000 INFO @ Sun, 21 Jun 2020 20:32:06: 27000000 INFO @ Sun, 21 Jun 2020 20:32:07: 21000000 INFO @ Sun, 21 Jun 2020 20:32:09: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:32:09: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:32:09: #1 total tags in treatment: 27649308 INFO @ Sun, 21 Jun 2020 20:32:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:09: #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 20:32:10: #1 tags after filtering in treatment: 27649261 INFO @ Sun, 21 Jun 2020 20:32:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:12: #2 number of paired peaks: 356 WARNING @ Sun, 21 Jun 2020 20:32:12: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sun, 21 Jun 2020 20:32:12: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:12: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:12: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:12: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:12: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:32:12: #2 alternative fragment length(s) may be 1,50 bps INFO @ Sun, 21 Jun 2020 20:32:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.10_model.r WARNING @ Sun, 21 Jun 2020 20:32:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:12: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Sun, 21 Jun 2020 20:32:12: #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 20:32:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:12: 22000000 INFO @ Sun, 21 Jun 2020 20:32:17: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:32:22: 24000000 INFO @ Sun, 21 Jun 2020 20:32:27: 25000000 INFO @ Sun, 21 Jun 2020 20:32:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:31: 26000000 INFO @ Sun, 21 Jun 2020 20:32:36: 27000000 INFO @ Sun, 21 Jun 2020 20:32:39: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:32:39: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:32:39: #1 total tags in treatment: 27649308 INFO @ Sun, 21 Jun 2020 20:32:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:39: #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 20:32:40: #1 tags after filtering in treatment: 27649261 INFO @ Sun, 21 Jun 2020 20:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:40: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:42: #2 number of paired peaks: 356 WARNING @ Sun, 21 Jun 2020 20:32:42: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sun, 21 Jun 2020 20:32:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:42: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:42: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:42: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:42: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 20:32:42: #2 alternative fragment length(s) may be 1,50 bps INFO @ Sun, 21 Jun 2020 20:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.20_model.r WARNING @ Sun, 21 Jun 2020 20:32:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:42: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Sun, 21 Jun 2020 20:32:42: #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 20:32:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:32:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:32:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.05_summits.bed INFO @ Sun, 21 Jun 2020 20:32:52: Done! pass1 - making usageList (614 chroms): 1 millis pass2 - checking and writing primary data (3546 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:32:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:33:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.10_summits.bed INFO @ Sun, 21 Jun 2020 20:33:22: Done! pass1 - making usageList (486 chroms): 1 millis pass2 - checking and writing primary data (1839 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:33:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981709/SRX3981709.20_summits.bed INFO @ Sun, 21 Jun 2020 20:33:54: Done! pass1 - making usageList (252 chroms): 1 millis pass2 - checking and writing primary data (618 records, 4 fields): 8 millis CompletedMACS2peakCalling