Job ID = 6453717 SRX = SRX1433360 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:28:11 prefetch.2.10.7: 1) Downloading 'SRR2919825'... 2020-06-21T08:28:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:40 prefetch.2.10.7: 1) 'SRR2919825' was downloaded successfully Read 29585896 spots for SRR2919825/SRR2919825.sra Written 29585896 spots for SRR2919825/SRR2919825.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:59 29585896 reads; of these: 29585896 (100.00%) were unpaired; of these: 755554 (2.55%) aligned 0 times 22693403 (76.70%) aligned exactly 1 time 6136939 (20.74%) aligned >1 times 97.45% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 5874139 / 28830342 = 0.2037 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 17:46:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.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 17:46:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:46:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:46:42: 1000000 INFO @ Sun, 21 Jun 2020 17:46:47: 2000000 INFO @ Sun, 21 Jun 2020 17:46:53: 3000000 INFO @ Sun, 21 Jun 2020 17:46:58: 4000000 INFO @ Sun, 21 Jun 2020 17:47:04: 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 17:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.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 17:47:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:10: 6000000 INFO @ Sun, 21 Jun 2020 17:47:11: 1000000 INFO @ Sun, 21 Jun 2020 17:47:15: 7000000 INFO @ Sun, 21 Jun 2020 17:47:17: 2000000 INFO @ Sun, 21 Jun 2020 17:47:21: 8000000 INFO @ Sun, 21 Jun 2020 17:47:22: 3000000 INFO @ Sun, 21 Jun 2020 17:47:27: 9000000 INFO @ Sun, 21 Jun 2020 17:47:28: 4000000 INFO @ Sun, 21 Jun 2020 17:47:33: 10000000 INFO @ Sun, 21 Jun 2020 17:47:34: 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 17:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.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 17:47:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:39: 11000000 INFO @ Sun, 21 Jun 2020 17:47:39: 6000000 INFO @ Sun, 21 Jun 2020 17:47:42: 1000000 INFO @ Sun, 21 Jun 2020 17:47:45: 12000000 INFO @ Sun, 21 Jun 2020 17:47:45: 7000000 INFO @ Sun, 21 Jun 2020 17:47:48: 2000000 INFO @ Sun, 21 Jun 2020 17:47:50: 8000000 INFO @ Sun, 21 Jun 2020 17:47:51: 13000000 INFO @ Sun, 21 Jun 2020 17:47:53: 3000000 INFO @ Sun, 21 Jun 2020 17:47:56: 9000000 INFO @ Sun, 21 Jun 2020 17:47:57: 14000000 INFO @ Sun, 21 Jun 2020 17:47:59: 4000000 INFO @ Sun, 21 Jun 2020 17:48:02: 10000000 INFO @ Sun, 21 Jun 2020 17:48:02: 15000000 INFO @ Sun, 21 Jun 2020 17:48:05: 5000000 INFO @ Sun, 21 Jun 2020 17:48:07: 11000000 INFO @ Sun, 21 Jun 2020 17:48:09: 16000000 INFO @ Sun, 21 Jun 2020 17:48:11: 6000000 INFO @ Sun, 21 Jun 2020 17:48:13: 12000000 INFO @ Sun, 21 Jun 2020 17:48:15: 17000000 INFO @ Sun, 21 Jun 2020 17:48:17: 7000000 INFO @ Sun, 21 Jun 2020 17:48:19: 13000000 INFO @ Sun, 21 Jun 2020 17:48:21: 18000000 INFO @ Sun, 21 Jun 2020 17:48:22: 8000000 INFO @ Sun, 21 Jun 2020 17:48:24: 14000000 INFO @ Sun, 21 Jun 2020 17:48:27: 19000000 INFO @ Sun, 21 Jun 2020 17:48:28: 9000000 INFO @ Sun, 21 Jun 2020 17:48:30: 15000000 INFO @ Sun, 21 Jun 2020 17:48:33: 20000000 INFO @ Sun, 21 Jun 2020 17:48:34: 10000000 INFO @ Sun, 21 Jun 2020 17:48:35: 16000000 INFO @ Sun, 21 Jun 2020 17:48:39: 21000000 INFO @ Sun, 21 Jun 2020 17:48:40: 11000000 INFO @ Sun, 21 Jun 2020 17:48:41: 17000000 INFO @ Sun, 21 Jun 2020 17:48:45: 22000000 INFO @ Sun, 21 Jun 2020 17:48:46: 12000000 INFO @ Sun, 21 Jun 2020 17:48:47: 18000000 INFO @ Sun, 21 Jun 2020 17:48:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:48:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:48:51: #1 total tags in treatment: 22956203 INFO @ Sun, 21 Jun 2020 17:48:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:51: #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 17:48:52: 13000000 INFO @ Sun, 21 Jun 2020 17:48:52: #1 tags after filtering in treatment: 22956134 INFO @ Sun, 21 Jun 2020 17:48:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:53: 19000000 INFO @ Sun, 21 Jun 2020 17:48:53: #2 number of paired peaks: 151 WARNING @ Sun, 21 Jun 2020 17:48:53: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sun, 21 Jun 2020 17:48:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:53: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:48:53: #2 alternative fragment length(s) may be 2,46,70 bps INFO @ Sun, 21 Jun 2020 17:48:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.05_model.r WARNING @ Sun, 21 Jun 2020 17:48:53: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:48:53: #2 You may need to consider one of the other alternative d(s): 2,46,70 WARNING @ Sun, 21 Jun 2020 17:48:53: #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 17:48:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:48:57: 14000000 INFO @ Sun, 21 Jun 2020 17:48:58: 20000000 INFO @ Sun, 21 Jun 2020 17:49:03: 15000000 INFO @ Sun, 21 Jun 2020 17:49:04: 21000000 INFO @ Sun, 21 Jun 2020 17:49:09: 16000000 INFO @ Sun, 21 Jun 2020 17:49:10: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:49:15: 17000000 INFO @ Sun, 21 Jun 2020 17:49:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:49:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:49:16: #1 total tags in treatment: 22956203 INFO @ Sun, 21 Jun 2020 17:49:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:16: #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 17:49:16: #1 tags after filtering in treatment: 22956134 INFO @ Sun, 21 Jun 2020 17:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:18: #2 number of paired peaks: 151 WARNING @ Sun, 21 Jun 2020 17:49:18: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sun, 21 Jun 2020 17:49:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:18: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:18: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:18: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:18: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:49:18: #2 alternative fragment length(s) may be 2,46,70 bps INFO @ Sun, 21 Jun 2020 17:49:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.10_model.r WARNING @ Sun, 21 Jun 2020 17:49:18: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:18: #2 You may need to consider one of the other alternative d(s): 2,46,70 WARNING @ Sun, 21 Jun 2020 17:49:18: #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 17:49:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:21: 18000000 INFO @ Sun, 21 Jun 2020 17:49:27: 19000000 INFO @ Sun, 21 Jun 2020 17:49:33: 20000000 INFO @ Sun, 21 Jun 2020 17:49:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:39: 21000000 INFO @ Sun, 21 Jun 2020 17:49:45: 22000000 INFO @ Sun, 21 Jun 2020 17:49:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:49:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:49:51: #1 total tags in treatment: 22956203 INFO @ Sun, 21 Jun 2020 17:49:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:51: #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 17:49:52: #1 tags after filtering in treatment: 22956134 INFO @ Sun, 21 Jun 2020 17:49:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:53: #2 number of paired peaks: 151 WARNING @ Sun, 21 Jun 2020 17:49:53: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sun, 21 Jun 2020 17:49:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:53: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:53: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:53: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:53: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 17:49:53: #2 alternative fragment length(s) may be 2,46,70 bps INFO @ Sun, 21 Jun 2020 17:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.20_model.r WARNING @ Sun, 21 Jun 2020 17:49:53: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:53: #2 You may need to consider one of the other alternative d(s): 2,46,70 WARNING @ Sun, 21 Jun 2020 17:49:53: #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 17:49:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:54: Done! pass1 - making usageList (274 chroms): 1 millis pass2 - checking and writing primary data (1151 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:50:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.10_summits.bed INFO @ Sun, 21 Jun 2020 17:50:17: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433360/SRX1433360.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:55: Done! pass1 - making usageList (64 chroms): 0 millis pass2 - checking and writing primary data (141 records, 4 fields): 4 millis CompletedMACS2peakCalling