Job ID = 6509067 SRX = SRX645110 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:07:00 prefetch.2.10.7: 1) Downloading 'SRR1505709'... 2020-06-26T15:07:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:13:56 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:13:56 prefetch.2.10.7: 1) 'SRR1505709' was downloaded successfully Read 40000000 spots for SRR1505709/SRR1505709.sra Written 40000000 spots for SRR1505709/SRR1505709.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: 00:13:06 40000000 reads; of these: 40000000 (100.00%) were unpaired; of these: 25198966 (63.00%) aligned 0 times 11280407 (28.20%) aligned exactly 1 time 3520627 (8.80%) aligned >1 times 37.00% overall alignment rate Time searching: 00:13:06 Overall time: 00:13:06 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] 9119993 / 14801034 = 0.6162 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 00:34:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.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 00:34:16: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:34:16: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:34:23: 1000000 INFO @ Sat, 27 Jun 2020 00:34:29: 2000000 INFO @ Sat, 27 Jun 2020 00:34:35: 3000000 INFO @ Sat, 27 Jun 2020 00:34:42: 4000000 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 00:34:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.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 00:34:46: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:34:46: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:34:49: 5000000 INFO @ Sat, 27 Jun 2020 00:34:53: 1000000 INFO @ Sat, 27 Jun 2020 00:34:54: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:34:54: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:34:54: #1 total tags in treatment: 5681041 INFO @ Sat, 27 Jun 2020 00:34:54: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:34:54: #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 00:34:54: #1 tags after filtering in treatment: 5681026 INFO @ Sat, 27 Jun 2020 00:34:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:34:54: #1 finished! INFO @ Sat, 27 Jun 2020 00:34:54: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:34:55: #2 number of paired peaks: 1027 INFO @ Sat, 27 Jun 2020 00:34:55: start model_add_line... INFO @ Sat, 27 Jun 2020 00:34:55: start X-correlation... INFO @ Sat, 27 Jun 2020 00:34:55: end of X-cor INFO @ Sat, 27 Jun 2020 00:34:55: #2 finished! INFO @ Sat, 27 Jun 2020 00:34:55: #2 predicted fragment length is 97 bps INFO @ Sat, 27 Jun 2020 00:34:55: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 27 Jun 2020 00:34:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.05_model.r WARNING @ Sat, 27 Jun 2020 00:34:55: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:34:55: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 27 Jun 2020 00:34:55: #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 00:34:55: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:35:00: 2000000 INFO @ Sat, 27 Jun 2020 00:35:06: 3000000 INFO @ Sat, 27 Jun 2020 00:35:08: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:35:13: 4000000 INFO @ Sat, 27 Jun 2020 00:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.05_summits.bed INFO @ Sat, 27 Jun 2020 00:35:14: Done! BedGraph に変換中... pass1 - making usageList (703 chroms): 1 millis pass2 - checking and writing primary data (2276 records, 4 fields): 22 millis 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 CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:35:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.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 00:35:16: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:35:16: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:35:20: 5000000 INFO @ Sat, 27 Jun 2020 00:35:23: 1000000 INFO @ Sat, 27 Jun 2020 00:35:25: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:35:25: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:35:25: #1 total tags in treatment: 5681041 INFO @ Sat, 27 Jun 2020 00:35:25: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:35:25: #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 00:35:26: #1 tags after filtering in treatment: 5681026 INFO @ Sat, 27 Jun 2020 00:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:35:26: #1 finished! INFO @ Sat, 27 Jun 2020 00:35:26: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:35:26: #2 number of paired peaks: 1027 INFO @ Sat, 27 Jun 2020 00:35:26: start model_add_line... INFO @ Sat, 27 Jun 2020 00:35:26: start X-correlation... INFO @ Sat, 27 Jun 2020 00:35:26: end of X-cor INFO @ Sat, 27 Jun 2020 00:35:26: #2 finished! INFO @ Sat, 27 Jun 2020 00:35:26: #2 predicted fragment length is 97 bps INFO @ Sat, 27 Jun 2020 00:35:26: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 27 Jun 2020 00:35:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.10_model.r WARNING @ Sat, 27 Jun 2020 00:35:26: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:35:26: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 27 Jun 2020 00:35:26: #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 00:35:26: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:35:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:35:30: 2000000 INFO @ Sat, 27 Jun 2020 00:35:36: 3000000 INFO @ Sat, 27 Jun 2020 00:35:38: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:35:43: 4000000 INFO @ Sat, 27 Jun 2020 00:35:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:35:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:35:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.10_summits.bed INFO @ Sat, 27 Jun 2020 00:35:44: Done! pass1 - making usageList (547 chroms): 1 millis pass2 - checking and writing primary data (1355 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:35:50: 5000000 INFO @ Sat, 27 Jun 2020 00:35:55: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:35:55: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:35:55: #1 total tags in treatment: 5681041 INFO @ Sat, 27 Jun 2020 00:35:55: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:35:55: #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 00:35:55: #1 tags after filtering in treatment: 5681026 INFO @ Sat, 27 Jun 2020 00:35:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:35:55: #1 finished! INFO @ Sat, 27 Jun 2020 00:35:55: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:35:55: #2 number of paired peaks: 1027 INFO @ Sat, 27 Jun 2020 00:35:55: start model_add_line... INFO @ Sat, 27 Jun 2020 00:35:56: start X-correlation... INFO @ Sat, 27 Jun 2020 00:35:56: end of X-cor INFO @ Sat, 27 Jun 2020 00:35:56: #2 finished! INFO @ Sat, 27 Jun 2020 00:35:56: #2 predicted fragment length is 97 bps INFO @ Sat, 27 Jun 2020 00:35:56: #2 alternative fragment length(s) may be 97 bps INFO @ Sat, 27 Jun 2020 00:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.20_model.r WARNING @ Sat, 27 Jun 2020 00:35:56: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:35:56: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sat, 27 Jun 2020 00:35:56: #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 00:35:56: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:35:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:36:08: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645110/SRX645110.20_summits.bed INFO @ Sat, 27 Jun 2020 00:36:14: Done! pass1 - making usageList (390 chroms): 1 millis pass2 - checking and writing primary data (741 records, 4 fields): 12 millis CompletedMACS2peakCalling