Job ID = 6459824 SRX = SRX864531 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:34:13 prefetch.2.10.7: 1) Downloading 'SRR1785671'... 2020-06-21T13:34:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:38:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:38:04 prefetch.2.10.7: 1) 'SRR1785671' was downloaded successfully 2020-06-21T13:38:04 prefetch.2.10.7: 'SRR1785671' has 0 unresolved dependencies Read 13765503 spots for SRR1785671/SRR1785671.sra Written 13765503 spots for SRR1785671/SRR1785671.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: 00:09:13 13765503 reads; of these: 13765503 (100.00%) were unpaired; of these: 808682 (5.87%) aligned 0 times 11155555 (81.04%) aligned exactly 1 time 1801266 (13.09%) aligned >1 times 94.13% overall alignment rate Time searching: 00:09:13 Overall time: 00:09:13 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] 2059421 / 12956821 = 0.1589 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 22:55:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.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 22:55:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:55:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:55:19: 1000000 INFO @ Sun, 21 Jun 2020 22:55:27: 2000000 INFO @ Sun, 21 Jun 2020 22:55:35: 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 22:55:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.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 22:55:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:55:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:55:44: 4000000 INFO @ Sun, 21 Jun 2020 22:55:49: 1000000 INFO @ Sun, 21 Jun 2020 22:55:53: 5000000 INFO @ Sun, 21 Jun 2020 22:55:58: 2000000 INFO @ Sun, 21 Jun 2020 22:56:01: 6000000 INFO @ Sun, 21 Jun 2020 22:56:06: 3000000 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 22:56:09: 7000000 INFO @ Sun, 21 Jun 2020 22:56:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.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 22:56:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:56:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:56:15: 4000000 INFO @ Sun, 21 Jun 2020 22:56:18: 8000000 INFO @ Sun, 21 Jun 2020 22:56:19: 1000000 INFO @ Sun, 21 Jun 2020 22:56:25: 5000000 INFO @ Sun, 21 Jun 2020 22:56:26: 9000000 INFO @ Sun, 21 Jun 2020 22:56:28: 2000000 INFO @ Sun, 21 Jun 2020 22:56:33: 6000000 INFO @ Sun, 21 Jun 2020 22:56:35: 10000000 INFO @ Sun, 21 Jun 2020 22:56:37: 3000000 INFO @ Sun, 21 Jun 2020 22:56:42: 7000000 INFO @ Sun, 21 Jun 2020 22:56:43: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 22:56:43: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 22:56:43: #1 total tags in treatment: 10897400 INFO @ Sun, 21 Jun 2020 22:56:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:56:43: #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 22:56:44: #1 tags after filtering in treatment: 10897325 INFO @ Sun, 21 Jun 2020 22:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:56:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:56:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:56:44: #2 number of paired peaks: 2751 INFO @ Sun, 21 Jun 2020 22:56:44: start model_add_line... INFO @ Sun, 21 Jun 2020 22:56:45: start X-correlation... INFO @ Sun, 21 Jun 2020 22:56:45: end of X-cor INFO @ Sun, 21 Jun 2020 22:56:45: #2 finished! INFO @ Sun, 21 Jun 2020 22:56:45: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 22:56:45: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 22:56:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.05_model.r WARNING @ Sun, 21 Jun 2020 22:56:45: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:56:45: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sun, 21 Jun 2020 22:56:45: #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 22:56:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:56:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:56:46: 4000000 INFO @ Sun, 21 Jun 2020 22:56:51: 8000000 INFO @ Sun, 21 Jun 2020 22:56:55: 5000000 INFO @ Sun, 21 Jun 2020 22:57:00: 9000000 INFO @ Sun, 21 Jun 2020 22:57:04: 6000000 INFO @ Sun, 21 Jun 2020 22:57:09: 10000000 INFO @ Sun, 21 Jun 2020 22:57:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:57:13: 7000000 INFO @ Sun, 21 Jun 2020 22:57:18: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 22:57:18: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 22:57:18: #1 total tags in treatment: 10897400 INFO @ Sun, 21 Jun 2020 22:57:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:57:18: #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 22:57:18: #1 tags after filtering in treatment: 10897325 INFO @ Sun, 21 Jun 2020 22:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:57:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:57:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:57:19: #2 number of paired peaks: 2751 INFO @ Sun, 21 Jun 2020 22:57:19: start model_add_line... INFO @ Sun, 21 Jun 2020 22:57:19: start X-correlation... INFO @ Sun, 21 Jun 2020 22:57:19: end of X-cor INFO @ Sun, 21 Jun 2020 22:57:19: #2 finished! INFO @ Sun, 21 Jun 2020 22:57:19: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 22:57:19: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 22:57:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.10_model.r WARNING @ Sun, 21 Jun 2020 22:57:19: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:57:19: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sun, 21 Jun 2020 22:57:19: #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 22:57:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:57:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:57:22: 8000000 INFO @ Sun, 21 Jun 2020 22:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.05_summits.bed INFO @ Sun, 21 Jun 2020 22:57:25: Done! pass1 - making usageList (412 chroms): 3 millis pass2 - checking and writing primary data (11439 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:57:30: 9000000 INFO @ Sun, 21 Jun 2020 22:57:39: 10000000 INFO @ Sun, 21 Jun 2020 22:57:47: #1 tag size is determined as 149 bps INFO @ Sun, 21 Jun 2020 22:57:47: #1 tag size = 149 INFO @ Sun, 21 Jun 2020 22:57:47: #1 total tags in treatment: 10897400 INFO @ Sun, 21 Jun 2020 22:57:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:57:47: #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 22:57:47: #1 tags after filtering in treatment: 10897325 INFO @ Sun, 21 Jun 2020 22:57:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:57:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:57:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:57:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:57:48: #2 number of paired peaks: 2751 INFO @ Sun, 21 Jun 2020 22:57:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:57:48: start X-correlation... INFO @ Sun, 21 Jun 2020 22:57:48: end of X-cor INFO @ Sun, 21 Jun 2020 22:57:48: #2 finished! INFO @ Sun, 21 Jun 2020 22:57:48: #2 predicted fragment length is 176 bps INFO @ Sun, 21 Jun 2020 22:57:48: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 21 Jun 2020 22:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.20_model.r WARNING @ Sun, 21 Jun 2020 22:57:48: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:57:48: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sun, 21 Jun 2020 22:57:48: #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 22:57:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:57:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:58:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:58:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.10_summits.bed INFO @ Sun, 21 Jun 2020 22:58:01: Done! pass1 - making usageList (264 chroms): 2 millis pass2 - checking and writing primary data (7636 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:58:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX864531/SRX864531.20_summits.bed INFO @ Sun, 21 Jun 2020 22:58:31: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (4335 records, 4 fields): 10 millis CompletedMACS2peakCalling