Job ID = 6453355 SRX = SRX1120690 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:25:26 prefetch.2.10.7: 1) Downloading 'SRR2129922'... 2020-06-21T08:25:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:29:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:29:59 prefetch.2.10.7: 1) 'SRR2129922' was downloaded successfully Read 17428295 spots for SRR2129922/SRR2129922.sra Written 17428295 spots for SRR2129922/SRR2129922.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: 00:08:46 17428295 reads; of these: 17428295 (100.00%) were unpaired; of these: 1332150 (7.64%) aligned 0 times 3991113 (22.90%) aligned exactly 1 time 12105032 (69.46%) aligned >1 times 92.36% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 6034815 / 16096145 = 0.3749 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 17:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.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 17:44:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:44: 1000000 INFO @ Sun, 21 Jun 2020 17:44:51: 2000000 INFO @ Sun, 21 Jun 2020 17:44:58: 3000000 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 17:45:05: 4000000 INFO @ Sun, 21 Jun 2020 17:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.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 17:45:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:13: 5000000 INFO @ Sun, 21 Jun 2020 17:45:16: 1000000 INFO @ Sun, 21 Jun 2020 17:45:22: 6000000 INFO @ Sun, 21 Jun 2020 17:45:26: 2000000 INFO @ Sun, 21 Jun 2020 17:45:32: 7000000 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 17:45:36: 3000000 INFO @ Sun, 21 Jun 2020 17:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.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 17:45:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:45:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:45:41: 8000000 INFO @ Sun, 21 Jun 2020 17:45:46: 4000000 INFO @ Sun, 21 Jun 2020 17:45:47: 1000000 INFO @ Sun, 21 Jun 2020 17:45:51: 9000000 INFO @ Sun, 21 Jun 2020 17:45:56: 5000000 INFO @ Sun, 21 Jun 2020 17:45:58: 2000000 INFO @ Sun, 21 Jun 2020 17:46:02: 10000000 INFO @ Sun, 21 Jun 2020 17:46:02: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:46:02: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:46:02: #1 total tags in treatment: 10061330 INFO @ Sun, 21 Jun 2020 17:46:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:02: #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 17:46:03: #1 tags after filtering in treatment: 10061284 INFO @ Sun, 21 Jun 2020 17:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:04: #2 number of paired peaks: 9051 INFO @ Sun, 21 Jun 2020 17:46:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:05: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 17:46:05: #2 alternative fragment length(s) may be 2,93 bps INFO @ Sun, 21 Jun 2020 17:46:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.05_model.r WARNING @ Sun, 21 Jun 2020 17:46:05: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:05: #2 You may need to consider one of the other alternative d(s): 2,93 WARNING @ Sun, 21 Jun 2020 17:46:05: #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 17:46:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:06: 6000000 INFO @ Sun, 21 Jun 2020 17:46:08: 3000000 INFO @ Sun, 21 Jun 2020 17:46:16: 7000000 INFO @ Sun, 21 Jun 2020 17:46:18: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:46:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:27: 8000000 INFO @ Sun, 21 Jun 2020 17:46:28: 5000000 INFO @ Sun, 21 Jun 2020 17:46:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:46:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:46:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.05_summits.bed INFO @ Sun, 21 Jun 2020 17:46:34: Done! pass1 - making usageList (1189 chroms): 1 millis pass2 - checking and writing primary data (5618 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:46:37: 9000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:46:38: 6000000 INFO @ Sun, 21 Jun 2020 17:46:48: 10000000 INFO @ Sun, 21 Jun 2020 17:46:48: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:46:48: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:46:48: #1 total tags in treatment: 10061330 INFO @ Sun, 21 Jun 2020 17:46:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:46:48: #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 17:46:49: 7000000 INFO @ Sun, 21 Jun 2020 17:46:49: #1 tags after filtering in treatment: 10061284 INFO @ Sun, 21 Jun 2020 17:46:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:46:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:46:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:46:50: #2 number of paired peaks: 9051 INFO @ Sun, 21 Jun 2020 17:46:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:46:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:46:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:46:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:46:50: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 17:46:50: #2 alternative fragment length(s) may be 2,93 bps INFO @ Sun, 21 Jun 2020 17:46:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.10_model.r WARNING @ Sun, 21 Jun 2020 17:46:50: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:46:50: #2 You may need to consider one of the other alternative d(s): 2,93 WARNING @ Sun, 21 Jun 2020 17:46:50: #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 17:46:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:46:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:46:58: 8000000 INFO @ Sun, 21 Jun 2020 17:47:07: 9000000 INFO @ Sun, 21 Jun 2020 17:47:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:16: 10000000 INFO @ Sun, 21 Jun 2020 17:47:17: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 17:47:17: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 17:47:17: #1 total tags in treatment: 10061330 INFO @ Sun, 21 Jun 2020 17:47:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:47:17: #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 17:47:17: #1 tags after filtering in treatment: 10061284 INFO @ Sun, 21 Jun 2020 17:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:47:17: #1 finished! INFO @ Sun, 21 Jun 2020 17:47:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:47:18: #2 number of paired peaks: 9051 INFO @ Sun, 21 Jun 2020 17:47:18: start model_add_line... INFO @ Sun, 21 Jun 2020 17:47:19: start X-correlation... INFO @ Sun, 21 Jun 2020 17:47:19: end of X-cor INFO @ Sun, 21 Jun 2020 17:47:19: #2 finished! INFO @ Sun, 21 Jun 2020 17:47:19: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 17:47:19: #2 alternative fragment length(s) may be 2,93 bps INFO @ Sun, 21 Jun 2020 17:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.20_model.r WARNING @ Sun, 21 Jun 2020 17:47:19: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:47:19: #2 You may need to consider one of the other alternative d(s): 2,93 WARNING @ Sun, 21 Jun 2020 17:47:19: #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 17:47:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:47:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.10_summits.bed INFO @ Sun, 21 Jun 2020 17:47:21: Done! pass1 - making usageList (979 chroms): 1 millis pass2 - checking and writing primary data (3011 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:47:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1120690/SRX1120690.20_summits.bed INFO @ Sun, 21 Jun 2020 17:47:49: Done! pass1 - making usageList (728 chroms): 2 millis pass2 - checking and writing primary data (1809 records, 4 fields): 19 millis CompletedMACS2peakCalling