Job ID = 6509232 SRX = SRX750081 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:18:28 prefetch.2.10.7: 1) Downloading 'SRR1638774'... 2020-06-26T15:18:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:30:50 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:30:50 prefetch.2.10.7: 1) 'SRR1638774' was downloaded successfully Read 55955788 spots for SRR1638774/SRR1638774.sra Written 55955788 spots for SRR1638774/SRR1638774.sra 2020-06-26T15:34:28 prefetch.2.10.7: 1) Downloading 'SRR1638775'... 2020-06-26T15:34:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:44:56 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:44:56 prefetch.2.10.7: 1) 'SRR1638775' was downloaded successfully Read 55027158 spots for SRR1638775/SRR1638775.sra Written 55027158 spots for SRR1638775/SRR1638775.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:09:09 110982946 reads; of these: 110982946 (100.00%) were unpaired; of these: 37092863 (33.42%) aligned 0 times 53063003 (47.81%) aligned exactly 1 time 20827080 (18.77%) aligned >1 times 66.58% overall alignment rate Time searching: 01:09:10 Overall time: 01:09:10 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 56 files... [bam_rmdupse_core] 71468952 / 73890083 = 0.9672 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 @ Sat, 27 Jun 2020 02:18:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.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 @ Sat, 27 Jun 2020 02:18:52: #1 read tag files... INFO @ Sat, 27 Jun 2020 02:18:52: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 02:18:59: 1000000 INFO @ Sat, 27 Jun 2020 02:19:07: 2000000 INFO @ Sat, 27 Jun 2020 02:19:10: #1 tag size is determined as 141 bps INFO @ Sat, 27 Jun 2020 02:19:10: #1 tag size = 141 INFO @ Sat, 27 Jun 2020 02:19:10: #1 total tags in treatment: 2421131 INFO @ Sat, 27 Jun 2020 02:19:10: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 02:19:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 02:19:10: #1 tags after filtering in treatment: 2420967 INFO @ Sat, 27 Jun 2020 02:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 02:19:10: #1 finished! INFO @ Sat, 27 Jun 2020 02:19:10: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 02:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 02:19:10: #2 number of paired peaks: 7913 INFO @ Sat, 27 Jun 2020 02:19:10: start model_add_line... INFO @ Sat, 27 Jun 2020 02:19:11: start X-correlation... INFO @ Sat, 27 Jun 2020 02:19:11: end of X-cor INFO @ Sat, 27 Jun 2020 02:19:11: #2 finished! INFO @ Sat, 27 Jun 2020 02:19:11: #2 predicted fragment length is 147 bps INFO @ Sat, 27 Jun 2020 02:19:11: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 27 Jun 2020 02:19:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.05_model.r WARNING @ Sat, 27 Jun 2020 02:19:11: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 02:19:11: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 27 Jun 2020 02:19:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 02:19:11: #3 Call peaks... INFO @ Sat, 27 Jun 2020 02:19:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 02:19:17: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 02:19:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.05_peaks.xls INFO @ Sat, 27 Jun 2020 02:19:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 02:19:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.05_summits.bed INFO @ Sat, 27 Jun 2020 02:19:20: Done! pass1 - making usageList (808 chroms): 2 millis pass2 - checking and writing primary data (3768 records, 4 fields): 22 millis CompletedMACS2peakCalling 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 @ Sat, 27 Jun 2020 02:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.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 @ Sat, 27 Jun 2020 02:19:22: #1 read tag files... INFO @ Sat, 27 Jun 2020 02:19:22: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 02:19:29: 1000000 INFO @ Sat, 27 Jun 2020 02:19:37: 2000000 INFO @ Sat, 27 Jun 2020 02:19:40: #1 tag size is determined as 141 bps INFO @ Sat, 27 Jun 2020 02:19:40: #1 tag size = 141 INFO @ Sat, 27 Jun 2020 02:19:40: #1 total tags in treatment: 2421131 INFO @ Sat, 27 Jun 2020 02:19:40: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 02:19:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 02:19:40: #1 tags after filtering in treatment: 2420967 INFO @ Sat, 27 Jun 2020 02:19:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 02:19:40: #1 finished! INFO @ Sat, 27 Jun 2020 02:19:40: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 02:19:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 02:19:40: #2 number of paired peaks: 7913 INFO @ Sat, 27 Jun 2020 02:19:40: start model_add_line... INFO @ Sat, 27 Jun 2020 02:19:40: start X-correlation... INFO @ Sat, 27 Jun 2020 02:19:40: end of X-cor INFO @ Sat, 27 Jun 2020 02:19:40: #2 finished! INFO @ Sat, 27 Jun 2020 02:19:40: #2 predicted fragment length is 147 bps INFO @ Sat, 27 Jun 2020 02:19:40: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 27 Jun 2020 02:19:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.10_model.r WARNING @ Sat, 27 Jun 2020 02:19:41: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 02:19:41: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 27 Jun 2020 02:19:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 02:19:41: #3 Call peaks... INFO @ Sat, 27 Jun 2020 02:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 02:19:47: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 02:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.10_peaks.xls INFO @ Sat, 27 Jun 2020 02:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 02:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.10_summits.bed INFO @ Sat, 27 Jun 2020 02:19:50: Done! pass1 - making usageList (652 chroms): 1 millis pass2 - checking and writing primary data (2048 records, 4 fields): 17 millis CompletedMACS2peakCalling 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 @ Sat, 27 Jun 2020 02:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.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 @ Sat, 27 Jun 2020 02:19:52: #1 read tag files... INFO @ Sat, 27 Jun 2020 02:19:52: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 02:19:59: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 02:20:07: 2000000 INFO @ Sat, 27 Jun 2020 02:20:10: #1 tag size is determined as 141 bps INFO @ Sat, 27 Jun 2020 02:20:10: #1 tag size = 141 INFO @ Sat, 27 Jun 2020 02:20:10: #1 total tags in treatment: 2421131 INFO @ Sat, 27 Jun 2020 02:20:10: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 02:20:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 02:20:10: #1 tags after filtering in treatment: 2420967 INFO @ Sat, 27 Jun 2020 02:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 02:20:10: #1 finished! INFO @ Sat, 27 Jun 2020 02:20:10: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 02:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 02:20:11: #2 number of paired peaks: 7913 INFO @ Sat, 27 Jun 2020 02:20:11: start model_add_line... INFO @ Sat, 27 Jun 2020 02:20:11: start X-correlation... INFO @ Sat, 27 Jun 2020 02:20:11: end of X-cor INFO @ Sat, 27 Jun 2020 02:20:11: #2 finished! INFO @ Sat, 27 Jun 2020 02:20:11: #2 predicted fragment length is 147 bps INFO @ Sat, 27 Jun 2020 02:20:11: #2 alternative fragment length(s) may be 147 bps INFO @ Sat, 27 Jun 2020 02:20:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.20_model.r WARNING @ Sat, 27 Jun 2020 02:20:11: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 02:20:11: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sat, 27 Jun 2020 02:20:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 02:20:11: #3 Call peaks... INFO @ Sat, 27 Jun 2020 02:20:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 02:20:17: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 02:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.20_peaks.xls INFO @ Sat, 27 Jun 2020 02:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 02:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750081/SRX750081.20_summits.bed INFO @ Sat, 27 Jun 2020 02:20:20: Done! pass1 - making usageList (496 chroms): 1 millis pass2 - checking and writing primary data (947 records, 4 fields): 13 millis CompletedMACS2peakCalling