Job ID = 6457250 SRX = SRX4579176 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:42:44 prefetch.2.10.7: 1) Downloading 'SRR7722319'... 2020-06-21T11:42:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:51:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:51:44 prefetch.2.10.7: 1) 'SRR7722319' was downloaded successfully 2020-06-21T11:51:44 prefetch.2.10.7: 'SRR7722319' has 0 unresolved dependencies Read 93741149 spots for SRR7722319/SRR7722319.sra Written 93741149 spots for SRR7722319/SRR7722319.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: 00:08:41 93741149 reads; of these: 93741149 (100.00%) were unpaired; of these: 93212085 (99.44%) aligned 0 times 343962 (0.37%) aligned exactly 1 time 185102 (0.20%) aligned >1 times 0.56% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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] 114700 / 529064 = 0.2168 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 21:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.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 21:06:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:06:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:07:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:07:02: #1 total tags in treatment: 414364 INFO @ Sun, 21 Jun 2020 21:07:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:02: #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 21:07:02: #1 tags after filtering in treatment: 413817 INFO @ Sun, 21 Jun 2020 21:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:02: #2 number of paired peaks: 3709 INFO @ Sun, 21 Jun 2020 21:07:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:02: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:07:02: #2 alternative fragment length(s) may be 49,163,191,229,290,369,513 bps INFO @ Sun, 21 Jun 2020 21:07:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.05_model.r WARNING @ Sun, 21 Jun 2020 21:07:02: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:07:02: #2 You may need to consider one of the other alternative d(s): 49,163,191,229,290,369,513 WARNING @ Sun, 21 Jun 2020 21:07:02: #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 21:07:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:07:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:07:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:07:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.05_summits.bed INFO @ Sun, 21 Jun 2020 21:07:04: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (464 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 21:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.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 21:07:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:07:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:07:32: #1 total tags in treatment: 414364 INFO @ Sun, 21 Jun 2020 21:07:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:32: #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 21:07:32: #1 tags after filtering in treatment: 413817 INFO @ Sun, 21 Jun 2020 21:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:32: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:32: #2 number of paired peaks: 3709 INFO @ Sun, 21 Jun 2020 21:07:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:32: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:07:32: #2 alternative fragment length(s) may be 49,163,191,229,290,369,513 bps INFO @ Sun, 21 Jun 2020 21:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.10_model.r WARNING @ Sun, 21 Jun 2020 21:07:33: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:07:33: #2 You may need to consider one of the other alternative d(s): 49,163,191,229,290,369,513 WARNING @ Sun, 21 Jun 2020 21:07:33: #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 21:07:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:07:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.10_summits.bed INFO @ Sun, 21 Jun 2020 21:07:34: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (272 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 21:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.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 21:07:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:59: #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 21:08:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:08:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:08:02: #1 total tags in treatment: 414364 INFO @ Sun, 21 Jun 2020 21:08:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:02: #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 21:08:02: #1 tags after filtering in treatment: 413817 INFO @ Sun, 21 Jun 2020 21:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:02: #2 number of paired peaks: 3709 INFO @ Sun, 21 Jun 2020 21:08:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:02: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 21:08:02: #2 alternative fragment length(s) may be 49,163,191,229,290,369,513 bps INFO @ Sun, 21 Jun 2020 21:08:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.20_model.r WARNING @ Sun, 21 Jun 2020 21:08:02: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:08:02: #2 You may need to consider one of the other alternative d(s): 49,163,191,229,290,369,513 WARNING @ Sun, 21 Jun 2020 21:08:02: #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 21:08:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:08:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579176/SRX4579176.20_summits.bed INFO @ Sun, 21 Jun 2020 21:08:04: Done! pass1 - making usageList (18 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 3 millis CompletedMACS2peakCalling