Job ID = 6457957 SRX = SRX4933869 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:19:49 prefetch.2.10.7: 1) Downloading 'SRR8107258'... 2020-06-21T12:19:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:22:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:22:28 prefetch.2.10.7: 1) 'SRR8107258' was downloaded successfully Read 23974614 spots for SRR8107258/SRR8107258.sra Written 23974614 spots for SRR8107258/SRR8107258.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: 00:06:56 23974614 reads; of these: 23974614 (100.00%) were unpaired; of these: 6773881 (28.25%) aligned 0 times 9250875 (38.59%) aligned exactly 1 time 7949858 (33.16%) aligned >1 times 71.75% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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] 12855766 / 17200733 = 0.7474 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 21:34:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.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 21:34:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:16: 1000000 INFO @ Sun, 21 Jun 2020 21:34:23: 2000000 INFO @ Sun, 21 Jun 2020 21:34:31: 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 21:34:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.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 21:34:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:34:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:34:38: 4000000 INFO @ Sun, 21 Jun 2020 21:34:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:34:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:34:41: #1 total tags in treatment: 4344967 INFO @ Sun, 21 Jun 2020 21:34:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:34:41: #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 21:34:42: #1 tags after filtering in treatment: 4344959 INFO @ Sun, 21 Jun 2020 21:34:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:34:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:34:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:34:42: #2 number of paired peaks: 2956 INFO @ Sun, 21 Jun 2020 21:34:42: start model_add_line... INFO @ Sun, 21 Jun 2020 21:34:42: start X-correlation... INFO @ Sun, 21 Jun 2020 21:34:42: end of X-cor INFO @ Sun, 21 Jun 2020 21:34:42: #2 finished! INFO @ Sun, 21 Jun 2020 21:34:42: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 21:34:42: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 21:34:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.05_model.r WARNING @ Sun, 21 Jun 2020 21:34:42: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:34:42: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 21:34:42: #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 21:34:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:34:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:46: 1000000 INFO @ Sun, 21 Jun 2020 21:34:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:34:54: 2000000 INFO @ Sun, 21 Jun 2020 21:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.05_summits.bed INFO @ Sun, 21 Jun 2020 21:34:56: Done! pass1 - making usageList (879 chroms): 2 millis pass2 - checking and writing primary data (3570 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:35:02: 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 21:35:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.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 21:35:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:35:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:35:10: 4000000 INFO @ Sun, 21 Jun 2020 21:35:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:35:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:35:13: #1 total tags in treatment: 4344967 INFO @ Sun, 21 Jun 2020 21:35:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:13: #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 21:35:13: #1 tags after filtering in treatment: 4344959 INFO @ Sun, 21 Jun 2020 21:35:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:13: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:13: #2 number of paired peaks: 2956 INFO @ Sun, 21 Jun 2020 21:35:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:13: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 21:35:13: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 21:35:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.10_model.r WARNING @ Sun, 21 Jun 2020 21:35:14: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:14: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 21:35:14: #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 21:35:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:17: 1000000 INFO @ Sun, 21 Jun 2020 21:35:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:24: 2000000 INFO @ Sun, 21 Jun 2020 21:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.10_summits.bed INFO @ Sun, 21 Jun 2020 21:35:28: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (680 chroms): 1 millis pass2 - checking and writing primary data (2585 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:35:32: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:35:39: 4000000 INFO @ Sun, 21 Jun 2020 21:35:42: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 21:35:42: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 21:35:42: #1 total tags in treatment: 4344967 INFO @ Sun, 21 Jun 2020 21:35:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:35:42: #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 21:35:42: #1 tags after filtering in treatment: 4344959 INFO @ Sun, 21 Jun 2020 21:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:35:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:35:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:35:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:35:43: #2 number of paired peaks: 2956 INFO @ Sun, 21 Jun 2020 21:35:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:35:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:35:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:35:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:35:43: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 21:35:43: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sun, 21 Jun 2020 21:35:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.20_model.r WARNING @ Sun, 21 Jun 2020 21:35:43: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:35:43: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sun, 21 Jun 2020 21:35:43: #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 21:35:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:35:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:35:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:35:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:35:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933869/SRX4933869.20_summits.bed INFO @ Sun, 21 Jun 2020 21:35:57: Done! pass1 - making usageList (530 chroms): 1 millis pass2 - checking and writing primary data (1290 records, 4 fields): 17 millis CompletedMACS2peakCalling