Job ID = 6453804 SRX = SRX149190 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:45:02 prefetch.2.10.7: 1) Downloading 'SRR500150'... 2020-06-21T08:45:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:49:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:49:07 prefetch.2.10.7: 'SRR500150' is valid 2020-06-21T08:49:07 prefetch.2.10.7: 1) 'SRR500150' was downloaded successfully Read 12993177 spots for SRR500150/SRR500150.sra Written 12993177 spots for SRR500150/SRR500150.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: 00:02:52 12993177 reads; of these: 12993177 (100.00%) were unpaired; of these: 5124797 (39.44%) aligned 0 times 4837328 (37.23%) aligned exactly 1 time 3031052 (23.33%) aligned >1 times 60.56% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 1554240 / 7868380 = 0.1975 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 17:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.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 17:54:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:53: 1000000 INFO @ Sun, 21 Jun 2020 17:54:59: 2000000 INFO @ Sun, 21 Jun 2020 17:55:04: 3000000 INFO @ Sun, 21 Jun 2020 17:55:10: 4000000 INFO @ Sun, 21 Jun 2020 17:55:15: 5000000 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 17:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.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 17:55:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:21: 6000000 INFO @ Sun, 21 Jun 2020 17:55:23: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:55:23: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:55:23: #1 total tags in treatment: 6314140 INFO @ Sun, 21 Jun 2020 17:55:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:23: #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 17:55:23: 1000000 INFO @ Sun, 21 Jun 2020 17:55:23: #1 tags after filtering in treatment: 6314036 INFO @ Sun, 21 Jun 2020 17:55:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:24: #2 number of paired peaks: 2127 INFO @ Sun, 21 Jun 2020 17:55:24: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:24: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:24: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:24: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:24: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 17:55:24: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 17:55:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.05_model.r WARNING @ Sun, 21 Jun 2020 17:55:24: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:55:24: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 17:55:24: #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 17:55:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:28: 2000000 INFO @ Sun, 21 Jun 2020 17:55:34: 3000000 INFO @ Sun, 21 Jun 2020 17:55:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:39: 4000000 INFO @ Sun, 21 Jun 2020 17:55:44: 5000000 INFO @ Sun, 21 Jun 2020 17:55:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.05_summits.bed INFO @ Sun, 21 Jun 2020 17:55:46: Done! pass1 - making usageList (603 chroms): 1 millis pass2 - checking and writing primary data (2856 records, 4 fields): 20 millis BedGraph に変換中... 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 17:55:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.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 17:55:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:49: 6000000 INFO @ Sun, 21 Jun 2020 17:55:51: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:55:51: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:55:51: #1 total tags in treatment: 6314140 INFO @ Sun, 21 Jun 2020 17:55:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:51: #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 17:55:51: #1 tags after filtering in treatment: 6314036 INFO @ Sun, 21 Jun 2020 17:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:52: #2 number of paired peaks: 2127 INFO @ Sun, 21 Jun 2020 17:55:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:52: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 17:55:52: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 17:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.10_model.r WARNING @ Sun, 21 Jun 2020 17:55:52: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:55:52: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 17:55:52: #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 17:55:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:53: 1000000 INFO @ Sun, 21 Jun 2020 17:55:58: 2000000 INFO @ Sun, 21 Jun 2020 17:56:03: 3000000 INFO @ Sun, 21 Jun 2020 17:56:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:08: 4000000 INFO @ Sun, 21 Jun 2020 17:56:13: 5000000 INFO @ Sun, 21 Jun 2020 17:56:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.10_summits.bed INFO @ Sun, 21 Jun 2020 17:56:14: Done! pass1 - making usageList (459 chroms): 1 millis pass2 - checking and writing primary data (1455 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:56:19: 6000000 INFO @ Sun, 21 Jun 2020 17:56:21: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:56:21: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:56:21: #1 total tags in treatment: 6314140 INFO @ Sun, 21 Jun 2020 17:56:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:21: #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 17:56:21: #1 tags after filtering in treatment: 6314036 INFO @ Sun, 21 Jun 2020 17:56:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:22: #2 number of paired peaks: 2127 INFO @ Sun, 21 Jun 2020 17:56:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:22: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 17:56:22: #2 alternative fragment length(s) may be 4,43 bps INFO @ Sun, 21 Jun 2020 17:56:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.20_model.r WARNING @ Sun, 21 Jun 2020 17:56:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:56:22: #2 You may need to consider one of the other alternative d(s): 4,43 WARNING @ Sun, 21 Jun 2020 17:56:22: #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 17:56:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:56:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149190/SRX149190.20_summits.bed INFO @ Sun, 21 Jun 2020 17:56:43: Done! pass1 - making usageList (160 chroms): 1 millis pass2 - checking and writing primary data (372 records, 4 fields): 8 millis CompletedMACS2peakCalling