Job ID = 6453813 SRX = SRX149199 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:39:32 prefetch.2.10.7: 1) Downloading 'SRR500159'... 2020-06-21T08:39:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:45:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:45:22 prefetch.2.10.7: 1) 'SRR500159' was downloaded successfully Read 24821883 spots for SRR500159/SRR500159.sra Written 24821883 spots for SRR500159/SRR500159.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: 00:05:56 24821883 reads; of these: 24821883 (100.00%) were unpaired; of these: 1328504 (5.35%) aligned 0 times 15931919 (64.18%) aligned exactly 1 time 7561460 (30.46%) aligned >1 times 94.65% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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 8 files... [bam_rmdupse_core] 4878596 / 23493379 = 0.2077 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 17:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.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 17:59:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:22: 1000000 INFO @ Sun, 21 Jun 2020 17:59:28: 2000000 INFO @ Sun, 21 Jun 2020 17:59:33: 3000000 INFO @ Sun, 21 Jun 2020 17:59:39: 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 17:59:44: 5000000 INFO @ Sun, 21 Jun 2020 17:59:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.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 17:59:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:50: 6000000 INFO @ Sun, 21 Jun 2020 17:59:52: 1000000 INFO @ Sun, 21 Jun 2020 17:59:56: 7000000 INFO @ Sun, 21 Jun 2020 17:59:59: 2000000 INFO @ Sun, 21 Jun 2020 18:00:03: 8000000 INFO @ Sun, 21 Jun 2020 18:00:05: 3000000 INFO @ Sun, 21 Jun 2020 18:00:09: 9000000 INFO @ Sun, 21 Jun 2020 18:00:11: 4000000 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 18:00:15: 10000000 INFO @ Sun, 21 Jun 2020 18:00:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.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 18:00:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:00:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:00:17: 5000000 INFO @ Sun, 21 Jun 2020 18:00:21: 11000000 INFO @ Sun, 21 Jun 2020 18:00:24: 6000000 INFO @ Sun, 21 Jun 2020 18:00:24: 1000000 INFO @ Sun, 21 Jun 2020 18:00:28: 12000000 INFO @ Sun, 21 Jun 2020 18:00:30: 7000000 INFO @ Sun, 21 Jun 2020 18:00:31: 2000000 INFO @ Sun, 21 Jun 2020 18:00:34: 13000000 INFO @ Sun, 21 Jun 2020 18:00:36: 8000000 INFO @ Sun, 21 Jun 2020 18:00:38: 3000000 INFO @ Sun, 21 Jun 2020 18:00:41: 14000000 INFO @ Sun, 21 Jun 2020 18:00:43: 9000000 INFO @ Sun, 21 Jun 2020 18:00:46: 4000000 INFO @ Sun, 21 Jun 2020 18:00:47: 15000000 INFO @ Sun, 21 Jun 2020 18:00:49: 10000000 INFO @ Sun, 21 Jun 2020 18:00:52: 5000000 INFO @ Sun, 21 Jun 2020 18:00:54: 16000000 INFO @ Sun, 21 Jun 2020 18:00:55: 11000000 INFO @ Sun, 21 Jun 2020 18:00:58: 6000000 INFO @ Sun, 21 Jun 2020 18:01:00: 17000000 INFO @ Sun, 21 Jun 2020 18:01:02: 12000000 INFO @ Sun, 21 Jun 2020 18:01:05: 7000000 INFO @ Sun, 21 Jun 2020 18:01:07: 18000000 INFO @ Sun, 21 Jun 2020 18:01:08: 13000000 INFO @ Sun, 21 Jun 2020 18:01:11: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:01:11: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:01:11: #1 total tags in treatment: 18614783 INFO @ Sun, 21 Jun 2020 18:01:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:11: #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 18:01:11: 8000000 INFO @ Sun, 21 Jun 2020 18:01:12: #1 tags after filtering in treatment: 18614739 INFO @ Sun, 21 Jun 2020 18:01:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:12: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:13: #2 number of paired peaks: 1241 INFO @ Sun, 21 Jun 2020 18:01:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:13: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:13: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:13: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:13: #2 predicted fragment length is 34 bps INFO @ Sun, 21 Jun 2020 18:01:13: #2 alternative fragment length(s) may be 1,34,590 bps INFO @ Sun, 21 Jun 2020 18:01:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.05_model.r WARNING @ Sun, 21 Jun 2020 18:01:13: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:13: #2 You may need to consider one of the other alternative d(s): 1,34,590 WARNING @ Sun, 21 Jun 2020 18:01:13: #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 18:01:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:14: 14000000 INFO @ Sun, 21 Jun 2020 18:01:17: 9000000 INFO @ Sun, 21 Jun 2020 18:01:20: 15000000 INFO @ Sun, 21 Jun 2020 18:01:24: 10000000 INFO @ Sun, 21 Jun 2020 18:01:27: 16000000 INFO @ Sun, 21 Jun 2020 18:01:30: 11000000 INFO @ Sun, 21 Jun 2020 18:01:33: 17000000 INFO @ Sun, 21 Jun 2020 18:01:36: 12000000 INFO @ Sun, 21 Jun 2020 18:01:38: 18000000 INFO @ Sun, 21 Jun 2020 18:01:42: 13000000 INFO @ Sun, 21 Jun 2020 18:01:42: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:01:42: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:01:42: #1 total tags in treatment: 18614783 INFO @ Sun, 21 Jun 2020 18:01:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:42: #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 18:01:43: #1 tags after filtering in treatment: 18614739 INFO @ Sun, 21 Jun 2020 18:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:45: #2 number of paired peaks: 1241 INFO @ Sun, 21 Jun 2020 18:01:45: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:45: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:45: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:45: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:45: #2 predicted fragment length is 34 bps INFO @ Sun, 21 Jun 2020 18:01:45: #2 alternative fragment length(s) may be 1,34,590 bps INFO @ Sun, 21 Jun 2020 18:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.10_model.r WARNING @ Sun, 21 Jun 2020 18:01:45: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:45: #2 You may need to consider one of the other alternative d(s): 1,34,590 WARNING @ Sun, 21 Jun 2020 18:01:45: #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 18:01:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:48: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:01:54: 15000000 INFO @ Sun, 21 Jun 2020 18:02:01: 16000000 INFO @ Sun, 21 Jun 2020 18:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.05_summits.bed INFO @ Sun, 21 Jun 2020 18:02:01: Done! pass1 - making usageList (633 chroms): 2 millis pass2 - checking and writing primary data (3460 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:02:06: 17000000 INFO @ Sun, 21 Jun 2020 18:02:12: 18000000 INFO @ Sun, 21 Jun 2020 18:02:16: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:02:16: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:02:16: #1 total tags in treatment: 18614783 INFO @ Sun, 21 Jun 2020 18:02:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:02:16: #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 18:02:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:17: #1 tags after filtering in treatment: 18614739 INFO @ Sun, 21 Jun 2020 18:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:02:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:02:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:02:18: #2 number of paired peaks: 1241 INFO @ Sun, 21 Jun 2020 18:02:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:02:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:02:19: end of X-cor INFO @ Sun, 21 Jun 2020 18:02:19: #2 finished! INFO @ Sun, 21 Jun 2020 18:02:19: #2 predicted fragment length is 34 bps INFO @ Sun, 21 Jun 2020 18:02:19: #2 alternative fragment length(s) may be 1,34,590 bps INFO @ Sun, 21 Jun 2020 18:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.20_model.r WARNING @ Sun, 21 Jun 2020 18:02:19: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:02:19: #2 You may need to consider one of the other alternative d(s): 1,34,590 WARNING @ Sun, 21 Jun 2020 18:02:19: #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 18:02:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.10_summits.bed INFO @ Sun, 21 Jun 2020 18:02:33: Done! pass1 - making usageList (503 chroms): 1 millis pass2 - checking and writing primary data (2005 records, 4 fields): 30 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:02:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:03:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:03:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149199/SRX149199.20_summits.bed INFO @ Sun, 21 Jun 2020 18:03:06: Done! pass1 - making usageList (184 chroms): 2 millis pass2 - checking and writing primary data (470 records, 4 fields): 22 millis CompletedMACS2peakCalling