Job ID = 6454624 SRX = SRX2422628 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:30:29 prefetch.2.10.7: 1) Downloading 'SRR5110242'... 2020-06-21T09:30:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:38:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:38:08 prefetch.2.10.7: 1) 'SRR5110242' was downloaded successfully Read 33068527 spots for SRR5110242/SRR5110242.sra Written 33068527 spots for SRR5110242/SRR5110242.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: 00:11:12 33068527 reads; of these: 33068527 (100.00%) were unpaired; of these: 1038278 (3.14%) aligned 0 times 22354164 (67.60%) aligned exactly 1 time 9676085 (29.26%) aligned >1 times 96.86% overall alignment rate Time searching: 00:11:12 Overall time: 00:11:12 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] 5144039 / 32030249 = 0.1606 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 18:59:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.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 18:59:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:15: 1000000 INFO @ Sun, 21 Jun 2020 18:59:22: 2000000 INFO @ Sun, 21 Jun 2020 18:59:29: 3000000 INFO @ Sun, 21 Jun 2020 18:59:35: 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 18:59:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.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 18:59:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:42: 5000000 INFO @ Sun, 21 Jun 2020 18:59:44: 1000000 INFO @ Sun, 21 Jun 2020 18:59:49: 6000000 INFO @ Sun, 21 Jun 2020 18:59:50: 2000000 INFO @ Sun, 21 Jun 2020 18:59:56: 7000000 INFO @ Sun, 21 Jun 2020 18:59:56: 3000000 INFO @ Sun, 21 Jun 2020 19:00:02: 4000000 INFO @ Sun, 21 Jun 2020 19:00:03: 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 19:00:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.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 19:00:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:00:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:00:08: 5000000 INFO @ Sun, 21 Jun 2020 19:00:10: 9000000 INFO @ Sun, 21 Jun 2020 19:00:14: 6000000 INFO @ Sun, 21 Jun 2020 19:00:15: 1000000 INFO @ Sun, 21 Jun 2020 19:00:17: 10000000 INFO @ Sun, 21 Jun 2020 19:00:20: 7000000 INFO @ Sun, 21 Jun 2020 19:00:21: 2000000 INFO @ Sun, 21 Jun 2020 19:00:24: 11000000 INFO @ Sun, 21 Jun 2020 19:00:27: 8000000 INFO @ Sun, 21 Jun 2020 19:00:28: 3000000 INFO @ Sun, 21 Jun 2020 19:00:32: 12000000 INFO @ Sun, 21 Jun 2020 19:00:33: 9000000 INFO @ Sun, 21 Jun 2020 19:00:35: 4000000 INFO @ Sun, 21 Jun 2020 19:00:38: 10000000 INFO @ Sun, 21 Jun 2020 19:00:39: 13000000 INFO @ Sun, 21 Jun 2020 19:00:41: 5000000 INFO @ Sun, 21 Jun 2020 19:00:44: 11000000 INFO @ Sun, 21 Jun 2020 19:00:46: 14000000 INFO @ Sun, 21 Jun 2020 19:00:48: 6000000 INFO @ Sun, 21 Jun 2020 19:00:50: 12000000 INFO @ Sun, 21 Jun 2020 19:00:53: 15000000 INFO @ Sun, 21 Jun 2020 19:00:54: 7000000 INFO @ Sun, 21 Jun 2020 19:00:56: 13000000 INFO @ Sun, 21 Jun 2020 19:00:59: 16000000 INFO @ Sun, 21 Jun 2020 19:01:01: 8000000 INFO @ Sun, 21 Jun 2020 19:01:02: 14000000 INFO @ Sun, 21 Jun 2020 19:01:06: 17000000 INFO @ Sun, 21 Jun 2020 19:01:07: 9000000 INFO @ Sun, 21 Jun 2020 19:01:08: 15000000 INFO @ Sun, 21 Jun 2020 19:01:13: 18000000 INFO @ Sun, 21 Jun 2020 19:01:14: 10000000 INFO @ Sun, 21 Jun 2020 19:01:14: 16000000 INFO @ Sun, 21 Jun 2020 19:01:20: 19000000 INFO @ Sun, 21 Jun 2020 19:01:20: 17000000 INFO @ Sun, 21 Jun 2020 19:01:20: 11000000 INFO @ Sun, 21 Jun 2020 19:01:26: 18000000 INFO @ Sun, 21 Jun 2020 19:01:27: 20000000 INFO @ Sun, 21 Jun 2020 19:01:27: 12000000 INFO @ Sun, 21 Jun 2020 19:01:32: 19000000 INFO @ Sun, 21 Jun 2020 19:01:33: 21000000 INFO @ Sun, 21 Jun 2020 19:01:34: 13000000 INFO @ Sun, 21 Jun 2020 19:01:38: 20000000 INFO @ Sun, 21 Jun 2020 19:01:40: 14000000 INFO @ Sun, 21 Jun 2020 19:01:40: 22000000 INFO @ Sun, 21 Jun 2020 19:01:44: 21000000 INFO @ Sun, 21 Jun 2020 19:01:47: 15000000 INFO @ Sun, 21 Jun 2020 19:01:47: 23000000 INFO @ Sun, 21 Jun 2020 19:01:50: 22000000 INFO @ Sun, 21 Jun 2020 19:01:53: 16000000 INFO @ Sun, 21 Jun 2020 19:01:54: 24000000 INFO @ Sun, 21 Jun 2020 19:01:56: 23000000 INFO @ Sun, 21 Jun 2020 19:02:00: 17000000 INFO @ Sun, 21 Jun 2020 19:02:01: 25000000 INFO @ Sun, 21 Jun 2020 19:02:02: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:02:06: 18000000 INFO @ Sun, 21 Jun 2020 19:02:08: 25000000 INFO @ Sun, 21 Jun 2020 19:02:08: 26000000 INFO @ Sun, 21 Jun 2020 19:02:13: 19000000 INFO @ Sun, 21 Jun 2020 19:02:14: 26000000 INFO @ Sun, 21 Jun 2020 19:02:15: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 19:02:15: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 19:02:15: #1 total tags in treatment: 26886210 INFO @ Sun, 21 Jun 2020 19:02:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:15: #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 19:02:15: #1 tags after filtering in treatment: 26886145 INFO @ Sun, 21 Jun 2020 19:02:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:17: #2 number of paired peaks: 678 WARNING @ Sun, 21 Jun 2020 19:02:17: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Sun, 21 Jun 2020 19:02:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:17: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:02:17: #2 alternative fragment length(s) may be 1,63,74 bps INFO @ Sun, 21 Jun 2020 19:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.05_model.r WARNING @ Sun, 21 Jun 2020 19:02:17: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:02:17: #2 You may need to consider one of the other alternative d(s): 1,63,74 WARNING @ Sun, 21 Jun 2020 19:02:17: #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 19:02:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:20: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 19:02:20: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 19:02:20: #1 total tags in treatment: 26886210 INFO @ Sun, 21 Jun 2020 19:02:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:02:20: #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 19:02:20: 20000000 INFO @ Sun, 21 Jun 2020 19:02:21: #1 tags after filtering in treatment: 26886145 INFO @ Sun, 21 Jun 2020 19:02:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:02:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:02:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:02:22: #2 number of paired peaks: 678 WARNING @ Sun, 21 Jun 2020 19:02:22: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Sun, 21 Jun 2020 19:02:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:02:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:02:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:02:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:02:23: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:02:23: #2 alternative fragment length(s) may be 1,63,74 bps INFO @ Sun, 21 Jun 2020 19:02:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.10_model.r WARNING @ Sun, 21 Jun 2020 19:02:23: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:02:23: #2 You may need to consider one of the other alternative d(s): 1,63,74 WARNING @ Sun, 21 Jun 2020 19:02:23: #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 19:02:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:02:27: 21000000 INFO @ Sun, 21 Jun 2020 19:02:33: 22000000 INFO @ Sun, 21 Jun 2020 19:02:40: 23000000 INFO @ Sun, 21 Jun 2020 19:02:47: 24000000 INFO @ Sun, 21 Jun 2020 19:02:53: 25000000 INFO @ Sun, 21 Jun 2020 19:03:00: 26000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:03:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:06: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 19:03:06: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 19:03:06: #1 total tags in treatment: 26886210 INFO @ Sun, 21 Jun 2020 19:03:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:06: #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 19:03:06: #1 tags after filtering in treatment: 26886145 INFO @ Sun, 21 Jun 2020 19:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:08: #2 number of paired peaks: 678 WARNING @ Sun, 21 Jun 2020 19:03:08: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Sun, 21 Jun 2020 19:03:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:08: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 19:03:08: #2 alternative fragment length(s) may be 1,63,74 bps INFO @ Sun, 21 Jun 2020 19:03:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.20_model.r WARNING @ Sun, 21 Jun 2020 19:03:08: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:03:08: #2 You may need to consider one of the other alternative d(s): 1,63,74 WARNING @ Sun, 21 Jun 2020 19:03:08: #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 19:03:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.05_summits.bed INFO @ Sun, 21 Jun 2020 19:03:28: Done! pass1 - making usageList (708 chroms): 2 millis pass2 - checking and writing primary data (3814 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:03:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.10_summits.bed INFO @ Sun, 21 Jun 2020 19:03:33: Done! pass1 - making usageList (555 chroms): 1 millis pass2 - checking and writing primary data (2076 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:03:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2422628/SRX2422628.20_summits.bed INFO @ Sun, 21 Jun 2020 19:04:19: Done! pass1 - making usageList (334 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 12 millis CompletedMACS2peakCalling