Job ID = 6454355 SRX = SRX201891 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:02:04 prefetch.2.10.7: 1) Downloading 'SRR609681'... 2020-06-21T09:02:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:06:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:06:08 prefetch.2.10.7: 1) 'SRR609681' was downloaded successfully Read 30914266 spots for SRR609681/SRR609681.sra Written 30914266 spots for SRR609681/SRR609681.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: 00:08:19 30914266 reads; of these: 30914266 (100.00%) were unpaired; of these: 956318 (3.09%) aligned 0 times 23562627 (76.22%) aligned exactly 1 time 6395321 (20.69%) aligned >1 times 96.91% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 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] 6338285 / 29957948 = 0.2116 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 18:23:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.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 18:23:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:23:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:23:44: 1000000 INFO @ Sun, 21 Jun 2020 18:23:50: 2000000 INFO @ Sun, 21 Jun 2020 18:23:57: 3000000 INFO @ Sun, 21 Jun 2020 18:24:04: 4000000 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 18:24:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.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 18:24:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:11: 5000000 INFO @ Sun, 21 Jun 2020 18:24:14: 1000000 INFO @ Sun, 21 Jun 2020 18:24:18: 6000000 INFO @ Sun, 21 Jun 2020 18:24:21: 2000000 INFO @ Sun, 21 Jun 2020 18:24:25: 7000000 INFO @ Sun, 21 Jun 2020 18:24:29: 3000000 INFO @ Sun, 21 Jun 2020 18:24:32: 8000000 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 18:24:36: 4000000 INFO @ Sun, 21 Jun 2020 18:24:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.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 18:24:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:39: 9000000 INFO @ Sun, 21 Jun 2020 18:24:44: 5000000 INFO @ Sun, 21 Jun 2020 18:24:44: 1000000 INFO @ Sun, 21 Jun 2020 18:24:47: 10000000 INFO @ Sun, 21 Jun 2020 18:24:51: 6000000 INFO @ Sun, 21 Jun 2020 18:24:52: 2000000 INFO @ Sun, 21 Jun 2020 18:24:54: 11000000 INFO @ Sun, 21 Jun 2020 18:24:59: 7000000 INFO @ Sun, 21 Jun 2020 18:25:00: 3000000 INFO @ Sun, 21 Jun 2020 18:25:02: 12000000 INFO @ Sun, 21 Jun 2020 18:25:06: 8000000 INFO @ Sun, 21 Jun 2020 18:25:07: 4000000 INFO @ Sun, 21 Jun 2020 18:25:10: 13000000 INFO @ Sun, 21 Jun 2020 18:25:13: 9000000 INFO @ Sun, 21 Jun 2020 18:25:15: 5000000 INFO @ Sun, 21 Jun 2020 18:25:17: 14000000 INFO @ Sun, 21 Jun 2020 18:25:21: 10000000 INFO @ Sun, 21 Jun 2020 18:25:22: 6000000 INFO @ Sun, 21 Jun 2020 18:25:24: 15000000 INFO @ Sun, 21 Jun 2020 18:25:28: 11000000 INFO @ Sun, 21 Jun 2020 18:25:29: 7000000 INFO @ Sun, 21 Jun 2020 18:25:32: 16000000 INFO @ Sun, 21 Jun 2020 18:25:36: 12000000 INFO @ Sun, 21 Jun 2020 18:25:37: 8000000 INFO @ Sun, 21 Jun 2020 18:25:39: 17000000 INFO @ Sun, 21 Jun 2020 18:25:43: 13000000 INFO @ Sun, 21 Jun 2020 18:25:44: 9000000 INFO @ Sun, 21 Jun 2020 18:25:46: 18000000 INFO @ Sun, 21 Jun 2020 18:25:50: 14000000 INFO @ Sun, 21 Jun 2020 18:25:52: 10000000 INFO @ Sun, 21 Jun 2020 18:25:54: 19000000 INFO @ Sun, 21 Jun 2020 18:25:58: 15000000 INFO @ Sun, 21 Jun 2020 18:25:59: 11000000 INFO @ Sun, 21 Jun 2020 18:26:02: 20000000 INFO @ Sun, 21 Jun 2020 18:26:05: 16000000 INFO @ Sun, 21 Jun 2020 18:26:06: 12000000 INFO @ Sun, 21 Jun 2020 18:26:09: 21000000 INFO @ Sun, 21 Jun 2020 18:26:12: 17000000 INFO @ Sun, 21 Jun 2020 18:26:14: 13000000 INFO @ Sun, 21 Jun 2020 18:26:17: 22000000 INFO @ Sun, 21 Jun 2020 18:26:19: 18000000 INFO @ Sun, 21 Jun 2020 18:26:21: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:26:24: 23000000 INFO @ Sun, 21 Jun 2020 18:26:27: 19000000 INFO @ Sun, 21 Jun 2020 18:26:28: 15000000 INFO @ Sun, 21 Jun 2020 18:26:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:26:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:26:29: #1 total tags in treatment: 23619663 INFO @ Sun, 21 Jun 2020 18:26:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:29: #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 18:26:30: #1 tags after filtering in treatment: 23619514 INFO @ Sun, 21 Jun 2020 18:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:32: #2 number of paired peaks: 688 WARNING @ Sun, 21 Jun 2020 18:26:32: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Sun, 21 Jun 2020 18:26:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:32: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:26:32: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 18:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.05_model.r WARNING @ Sun, 21 Jun 2020 18:26:32: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:26:32: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 18:26:32: #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 18:26:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:26:35: 20000000 INFO @ Sun, 21 Jun 2020 18:26:36: 16000000 INFO @ Sun, 21 Jun 2020 18:26:42: 21000000 INFO @ Sun, 21 Jun 2020 18:26:43: 17000000 INFO @ Sun, 21 Jun 2020 18:26:49: 22000000 INFO @ Sun, 21 Jun 2020 18:26:50: 18000000 INFO @ Sun, 21 Jun 2020 18:26:56: 23000000 INFO @ Sun, 21 Jun 2020 18:26:58: 19000000 INFO @ Sun, 21 Jun 2020 18:27:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:27:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:27:01: #1 total tags in treatment: 23619663 INFO @ Sun, 21 Jun 2020 18:27:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:01: #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 18:27:02: #1 tags after filtering in treatment: 23619514 INFO @ Sun, 21 Jun 2020 18:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:03: #2 number of paired peaks: 688 WARNING @ Sun, 21 Jun 2020 18:27:03: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:04: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:27:04: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 18:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.10_model.r WARNING @ Sun, 21 Jun 2020 18:27:04: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:04: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 18:27:04: #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 18:27:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:05: 20000000 INFO @ Sun, 21 Jun 2020 18:27:12: 21000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:27:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:19: 22000000 INFO @ Sun, 21 Jun 2020 18:27:26: 23000000 INFO @ Sun, 21 Jun 2020 18:27:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:27:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:27:30: #1 total tags in treatment: 23619663 INFO @ Sun, 21 Jun 2020 18:27:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:30: #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 18:27:31: #1 tags after filtering in treatment: 23619514 INFO @ Sun, 21 Jun 2020 18:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:32: #2 number of paired peaks: 688 WARNING @ Sun, 21 Jun 2020 18:27:32: Fewer paired peaks (688) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 688 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:33: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:27:33: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 18:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.20_model.r WARNING @ Sun, 21 Jun 2020 18:27:33: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:33: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 18:27:33: #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 18:27:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.05_summits.bed INFO @ Sun, 21 Jun 2020 18:27:43: Done! pass1 - making usageList (735 chroms): 1 millis pass2 - checking and writing primary data (5077 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:27:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.10_summits.bed INFO @ Sun, 21 Jun 2020 18:28:12: Done! pass1 - making usageList (623 chroms): 1 millis pass2 - checking and writing primary data (2773 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201891/SRX201891.20_summits.bed INFO @ Sun, 21 Jun 2020 18:28:41: Done! pass1 - making usageList (494 chroms): 1 millis pass2 - checking and writing primary data (1722 records, 4 fields): 16 millis CompletedMACS2peakCalling