Job ID = 6456002 SRX = SRX315133 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:51 prefetch.2.10.7: 1) Downloading 'SRR922189'... 2020-06-21T10:30:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:32:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:32:45 prefetch.2.10.7: 'SRR922189' is valid 2020-06-21T10:32:45 prefetch.2.10.7: 1) 'SRR922189' was downloaded successfully 2020-06-21T10:32:45 prefetch.2.10.7: 'SRR922189' has 0 unresolved dependencies Read 4745448 spots for SRR922189/SRR922189.sra Written 4745448 spots for SRR922189/SRR922189.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: 00:02:41 4745448 reads; of these: 4745448 (100.00%) were unpaired; of these: 1265126 (26.66%) aligned 0 times 2736034 (57.66%) aligned exactly 1 time 744288 (15.68%) aligned >1 times 73.34% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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_rmdupse_core] 986922 / 3480322 = 0.2836 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 19:38:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.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 19:38:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:16: 1000000 INFO @ Sun, 21 Jun 2020 19:38:25: 2000000 INFO @ Sun, 21 Jun 2020 19:38:29: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 19:38:29: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 19:38:29: #1 total tags in treatment: 2493400 INFO @ Sun, 21 Jun 2020 19:38:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:29: #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 19:38:30: #1 tags after filtering in treatment: 2493085 INFO @ Sun, 21 Jun 2020 19:38:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:30: #2 number of paired peaks: 4728 INFO @ Sun, 21 Jun 2020 19:38:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:30: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:38:30: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 19:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.05_model.r WARNING @ Sun, 21 Jun 2020 19:38:30: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:38:30: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sun, 21 Jun 2020 19:38:30: #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 19:38:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:30: #3 Pre-compute pvalue-qvalue table... 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 19:38:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.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 19:38:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:38:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:38:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:40: Done! pass1 - making usageList (102 chroms): 2 millis pass2 - checking and writing primary data (4928 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:46: 1000000 INFO @ Sun, 21 Jun 2020 19:38:55: 2000000 INFO @ Sun, 21 Jun 2020 19:38:59: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 19:38:59: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 19:38:59: #1 total tags in treatment: 2493400 INFO @ Sun, 21 Jun 2020 19:38:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:59: #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 19:38:59: #1 tags after filtering in treatment: 2493085 INFO @ Sun, 21 Jun 2020 19:38:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:59: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:00: #2 number of paired peaks: 4728 INFO @ Sun, 21 Jun 2020 19:39:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:00: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:39:00: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 19:39:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.10_model.r WARNING @ Sun, 21 Jun 2020 19:39:00: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:00: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sun, 21 Jun 2020 19:39:00: #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 19:39:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:00: #3 Pre-compute pvalue-qvalue table... 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 19:39:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.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 19:39:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:39:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.10_summits.bed INFO @ Sun, 21 Jun 2020 19:39:11: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (3722 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:16: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:39:25: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:39:29: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 19:39:29: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 19:39:29: #1 total tags in treatment: 2493400 INFO @ Sun, 21 Jun 2020 19:39:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:39:29: #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 19:39:29: #1 tags after filtering in treatment: 2493085 INFO @ Sun, 21 Jun 2020 19:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:39:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:39:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:39:29: #2 number of paired peaks: 4728 INFO @ Sun, 21 Jun 2020 19:39:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:39:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:39:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:39:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:39:30: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:39:30: #2 alternative fragment length(s) may be 216 bps INFO @ Sun, 21 Jun 2020 19:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.20_model.r WARNING @ Sun, 21 Jun 2020 19:39:30: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:39:30: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Sun, 21 Jun 2020 19:39:30: #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 19:39:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:39:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX315133/SRX315133.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:41: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (2517 records, 4 fields): 4 millis CompletedMACS2peakCalling