Job ID = 6456487 SRX = SRX348472 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:51:46 prefetch.2.10.7: 1) Downloading 'SRR976156'... 2020-06-21T10:51:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:54:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:54:05 prefetch.2.10.7: 'SRR976156' is valid 2020-06-21T10:54:05 prefetch.2.10.7: 1) 'SRR976156' was downloaded successfully Read 12741923 spots for SRR976156/SRR976156.sra Written 12741923 spots for SRR976156/SRR976156.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: 00:01:01 12741923 reads; of these: 12741923 (100.00%) were unpaired; of these: 12330425 (96.77%) aligned 0 times 335200 (2.63%) aligned exactly 1 time 76298 (0.60%) aligned >1 times 3.23% overall alignment rate Time searching: 00:01:01 Overall time: 00:01:01 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] 74227 / 411498 = 0.1804 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 19:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.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 19:56:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:25: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:56:25: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:56:25: #1 total tags in treatment: 337271 INFO @ Sun, 21 Jun 2020 19:56:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:25: #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 19:56:25: #1 tags after filtering in treatment: 336675 INFO @ Sun, 21 Jun 2020 19:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:25: #2 number of paired peaks: 4675 INFO @ Sun, 21 Jun 2020 19:56:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:25: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:56:25: #2 alternative fragment length(s) may be 35,134,487,539,583 bps INFO @ Sun, 21 Jun 2020 19:56:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.05_model.r WARNING @ Sun, 21 Jun 2020 19:56:25: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:25: #2 You may need to consider one of the other alternative d(s): 35,134,487,539,583 WARNING @ Sun, 21 Jun 2020 19:56:25: #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 19:56:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.05_summits.bed INFO @ Sun, 21 Jun 2020 19:56:26: Done! pass1 - making usageList (73 chroms): 1 millis pass2 - checking and writing primary data (1192 records, 4 fields): 5 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 @ Sun, 21 Jun 2020 19:56:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.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 19:56:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:55: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:56:55: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:56:55: #1 total tags in treatment: 337271 INFO @ Sun, 21 Jun 2020 19:56:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:55: #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 19:56:55: #1 tags after filtering in treatment: 336675 INFO @ Sun, 21 Jun 2020 19:56:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:56:55: #2 number of paired peaks: 4675 INFO @ Sun, 21 Jun 2020 19:56:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:55: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:56:55: #2 alternative fragment length(s) may be 35,134,487,539,583 bps INFO @ Sun, 21 Jun 2020 19:56:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.10_model.r WARNING @ Sun, 21 Jun 2020 19:56:55: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:55: #2 You may need to consider one of the other alternative d(s): 35,134,487,539,583 WARNING @ Sun, 21 Jun 2020 19:56:55: #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 19:56:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.10_summits.bed INFO @ Sun, 21 Jun 2020 19:56:56: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 2 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 @ Sun, 21 Jun 2020 19:57:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.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 19:57:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:23: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:57:25: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:57:25: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:57:25: #1 total tags in treatment: 337271 INFO @ Sun, 21 Jun 2020 19:57:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:25: #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 19:57:25: #1 tags after filtering in treatment: 336675 INFO @ Sun, 21 Jun 2020 19:57:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:25: #2 number of paired peaks: 4675 INFO @ Sun, 21 Jun 2020 19:57:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:25: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:57:25: #2 alternative fragment length(s) may be 35,134,487,539,583 bps INFO @ Sun, 21 Jun 2020 19:57:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.20_model.r WARNING @ Sun, 21 Jun 2020 19:57:25: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:25: #2 You may need to consider one of the other alternative d(s): 35,134,487,539,583 WARNING @ Sun, 21 Jun 2020 19:57:25: #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 19:57:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348472/SRX348472.20_summits.bed INFO @ Sun, 21 Jun 2020 19:57:27: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 2 millis CompletedMACS2peakCalling