Job ID = 6456488 SRX = SRX348473 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:49:01 prefetch.2.10.7: 1) Downloading 'SRR976157'... 2020-06-21T10:49:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:51:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:51:45 prefetch.2.10.7: 'SRR976157' is valid 2020-06-21T10:51:45 prefetch.2.10.7: 1) 'SRR976157' was downloaded successfully Read 16078182 spots for SRR976157/SRR976157.sra Written 16078182 spots for SRR976157/SRR976157.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: 00:01:15 16078182 reads; of these: 16078182 (100.00%) were unpaired; of these: 15615519 (97.12%) aligned 0 times 370052 (2.30%) aligned exactly 1 time 92611 (0.58%) aligned >1 times 2.88% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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] 117455 / 462663 = 0.2539 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 19:54:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.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 19:54:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:24: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:54:24: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:54:24: #1 total tags in treatment: 345208 INFO @ Sun, 21 Jun 2020 19:54:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:24: #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 19:54:24: #1 tags after filtering in treatment: 344789 INFO @ Sun, 21 Jun 2020 19:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:24: #2 number of paired peaks: 5256 INFO @ Sun, 21 Jun 2020 19:54:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:24: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:54:24: #2 alternative fragment length(s) may be 35,208,551,582,596 bps INFO @ Sun, 21 Jun 2020 19:54:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.05_model.r WARNING @ Sun, 21 Jun 2020 19:54:24: #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 19:54:24: #2 You may need to consider one of the other alternative d(s): 35,208,551,582,596 WARNING @ Sun, 21 Jun 2020 19:54:24: #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 19:54:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.05_summits.bed INFO @ Sun, 21 Jun 2020 19:54:26: Done! pass1 - making usageList (83 chroms): 1 millis pass2 - checking and writing primary data (1121 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 19:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.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 19:54:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:54:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:54:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:54:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:54:54: #1 total tags in treatment: 345208 INFO @ Sun, 21 Jun 2020 19:54:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:54: #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 19:54:54: #1 tags after filtering in treatment: 344789 INFO @ Sun, 21 Jun 2020 19:54:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:54: #2 number of paired peaks: 5256 INFO @ Sun, 21 Jun 2020 19:54:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:54: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:54:54: #2 alternative fragment length(s) may be 35,208,551,582,596 bps INFO @ Sun, 21 Jun 2020 19:54:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.10_model.r WARNING @ Sun, 21 Jun 2020 19:54:54: #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 19:54:54: #2 You may need to consider one of the other alternative d(s): 35,208,551,582,596 WARNING @ Sun, 21 Jun 2020 19:54:54: #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 19:54:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.10_summits.bed INFO @ Sun, 21 Jun 2020 19:54:56: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 4 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 19:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.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 19:55:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:22: #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 19:55:24: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 19:55:24: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 19:55:24: #1 total tags in treatment: 345208 INFO @ Sun, 21 Jun 2020 19:55:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:55:24: #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 19:55:24: #1 tags after filtering in treatment: 344789 INFO @ Sun, 21 Jun 2020 19:55:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:55:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:55:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:55:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:55:24: #2 number of paired peaks: 5256 INFO @ Sun, 21 Jun 2020 19:55:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:55:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:55:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:55:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:55:24: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:55:24: #2 alternative fragment length(s) may be 35,208,551,582,596 bps INFO @ Sun, 21 Jun 2020 19:55:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.20_model.r WARNING @ Sun, 21 Jun 2020 19:55:24: #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 19:55:24: #2 You may need to consider one of the other alternative d(s): 35,208,551,582,596 WARNING @ Sun, 21 Jun 2020 19:55:24: #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 19:55:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:55:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:55:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX348473/SRX348473.20_summits.bed INFO @ Sun, 21 Jun 2020 19:55:26: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 3 millis CompletedMACS2peakCalling