Job ID = 6459218 SRX = SRX645130 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:07:01 prefetch.2.10.7: 1) Downloading 'SRR1505730'... 2020-06-21T13:07:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:17:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:17:12 prefetch.2.10.7: 1) 'SRR1505730' was downloaded successfully Read 29810300 spots for SRR1505730/SRR1505730.sra Written 29810300 spots for SRR1505730/SRR1505730.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: 00:09:33 29810300 reads; of these: 29810300 (100.00%) were unpaired; of these: 22980751 (77.09%) aligned 0 times 5060420 (16.98%) aligned exactly 1 time 1769129 (5.93%) aligned >1 times 22.91% overall alignment rate Time searching: 00:09:33 Overall time: 00:09:33 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] 5770533 / 6829549 = 0.8449 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 22:30:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.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 22:30:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:30:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:31:00: 1000000 INFO @ Sun, 21 Jun 2020 22:31:01: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:31:01: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:31:01: #1 total tags in treatment: 1059016 INFO @ Sun, 21 Jun 2020 22:31:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:31:01: #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 22:31:01: #1 tags after filtering in treatment: 1058812 INFO @ Sun, 21 Jun 2020 22:31:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:31:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:31:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:31:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:31:01: #2 number of paired peaks: 3125 INFO @ Sun, 21 Jun 2020 22:31:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:31:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:31:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:31:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:31:01: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 22:31:01: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 22:31:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.05_model.r WARNING @ Sun, 21 Jun 2020 22:31:01: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:31:01: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sun, 21 Jun 2020 22:31:01: #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 22:31:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:31:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:31:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:31:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:31:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:31:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.05_summits.bed INFO @ Sun, 21 Jun 2020 22:31:06: Done! pass1 - making usageList (541 chroms): 2 millis pass2 - checking and writing primary data (1242 records, 4 fields): 16 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 22:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.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 22:31:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:31:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:31:30: 1000000 INFO @ Sun, 21 Jun 2020 22:31:30: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:31:30: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:31:30: #1 total tags in treatment: 1059016 INFO @ Sun, 21 Jun 2020 22:31:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:31:30: #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 22:31:31: #1 tags after filtering in treatment: 1058812 INFO @ Sun, 21 Jun 2020 22:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:31:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:31:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:31:31: #2 number of paired peaks: 3125 INFO @ Sun, 21 Jun 2020 22:31:31: start model_add_line... INFO @ Sun, 21 Jun 2020 22:31:31: start X-correlation... INFO @ Sun, 21 Jun 2020 22:31:31: end of X-cor INFO @ Sun, 21 Jun 2020 22:31:31: #2 finished! INFO @ Sun, 21 Jun 2020 22:31:31: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 22:31:31: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 22:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.10_model.r WARNING @ Sun, 21 Jun 2020 22:31:31: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:31:31: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sun, 21 Jun 2020 22:31:31: #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 22:31:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:31:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:31:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:31:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:31:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.10_summits.bed INFO @ Sun, 21 Jun 2020 22:31:36: Done! pass1 - making usageList (408 chroms): 1 millis pass2 - checking and writing primary data (685 records, 4 fields): 13 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 22:31:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.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 22:31:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:31:51: #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 22:32:00: 1000000 INFO @ Sun, 21 Jun 2020 22:32:00: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:32:00: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:32:00: #1 total tags in treatment: 1059016 INFO @ Sun, 21 Jun 2020 22:32:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:32:00: #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 22:32:01: #1 tags after filtering in treatment: 1058812 INFO @ Sun, 21 Jun 2020 22:32:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:32:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:32:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:32:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:32:01: #2 number of paired peaks: 3125 INFO @ Sun, 21 Jun 2020 22:32:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:32:01: start X-correlation... INFO @ Sun, 21 Jun 2020 22:32:01: end of X-cor INFO @ Sun, 21 Jun 2020 22:32:01: #2 finished! INFO @ Sun, 21 Jun 2020 22:32:01: #2 predicted fragment length is 103 bps INFO @ Sun, 21 Jun 2020 22:32:01: #2 alternative fragment length(s) may be 103 bps INFO @ Sun, 21 Jun 2020 22:32:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.20_model.r WARNING @ Sun, 21 Jun 2020 22:32:01: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:32:01: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sun, 21 Jun 2020 22:32:01: #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 22:32:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:32:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:32:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:32:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:32:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:32:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645130/SRX645130.20_summits.bed INFO @ Sun, 21 Jun 2020 22:32:05: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 6 millis CompletedMACS2peakCalling