Job ID = 6453810 SRX = SRX149196 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:38:09 prefetch.2.10.7: 1) Downloading 'SRR500156'... 2020-06-21T08:38:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:40:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:40:39 prefetch.2.10.7: 'SRR500156' is valid 2020-06-21T08:40:39 prefetch.2.10.7: 1) 'SRR500156' was downloaded successfully Read 12688184 spots for SRR500156/SRR500156.sra Written 12688184 spots for SRR500156/SRR500156.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: 00:03:13 12688184 reads; of these: 12688184 (100.00%) were unpaired; of these: 529115 (4.17%) aligned 0 times 7890768 (62.19%) aligned exactly 1 time 4268301 (33.64%) aligned >1 times 95.83% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 2136308 / 12159069 = 0.1757 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 17:47:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.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 17:47:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:47:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:47:36: 1000000 INFO @ Sun, 21 Jun 2020 17:47:41: 2000000 INFO @ Sun, 21 Jun 2020 17:47:46: 3000000 INFO @ Sun, 21 Jun 2020 17:47:51: 4000000 INFO @ Sun, 21 Jun 2020 17:47:57: 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 17:48:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.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 17:48:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:02: 6000000 INFO @ Sun, 21 Jun 2020 17:48:06: 1000000 INFO @ Sun, 21 Jun 2020 17:48:08: 7000000 INFO @ Sun, 21 Jun 2020 17:48:12: 2000000 INFO @ Sun, 21 Jun 2020 17:48:13: 8000000 INFO @ Sun, 21 Jun 2020 17:48:18: 3000000 INFO @ Sun, 21 Jun 2020 17:48:19: 9000000 INFO @ Sun, 21 Jun 2020 17:48:24: 4000000 INFO @ Sun, 21 Jun 2020 17:48:25: 10000000 INFO @ Sun, 21 Jun 2020 17:48:25: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:48:25: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:48:25: #1 total tags in treatment: 10022761 INFO @ Sun, 21 Jun 2020 17:48:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:48:25: #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 17:48:26: #1 tags after filtering in treatment: 10022673 INFO @ Sun, 21 Jun 2020 17:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:48:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:48:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:48:27: #2 number of paired peaks: 1898 INFO @ Sun, 21 Jun 2020 17:48:27: start model_add_line... INFO @ Sun, 21 Jun 2020 17:48:27: start X-correlation... INFO @ Sun, 21 Jun 2020 17:48:27: end of X-cor INFO @ Sun, 21 Jun 2020 17:48:27: #2 finished! INFO @ Sun, 21 Jun 2020 17:48:27: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 17:48:27: #2 alternative fragment length(s) may be 2,39,575 bps INFO @ Sun, 21 Jun 2020 17:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.05_model.r WARNING @ Sun, 21 Jun 2020 17:48:27: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:48:27: #2 You may need to consider one of the other alternative d(s): 2,39,575 WARNING @ Sun, 21 Jun 2020 17:48:27: #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 17:48:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:48:27: #3 Pre-compute pvalue-qvalue table... 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 17:48:29: 5000000 INFO @ Sun, 21 Jun 2020 17:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.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 17:48:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:48:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:48:35: 6000000 INFO @ Sun, 21 Jun 2020 17:48:37: 1000000 INFO @ Sun, 21 Jun 2020 17:48:42: 7000000 INFO @ Sun, 21 Jun 2020 17:48:42: 2000000 INFO @ Sun, 21 Jun 2020 17:48:47: 8000000 INFO @ Sun, 21 Jun 2020 17:48:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:48:48: 3000000 INFO @ Sun, 21 Jun 2020 17:48:54: 9000000 INFO @ Sun, 21 Jun 2020 17:48:54: 4000000 INFO @ Sun, 21 Jun 2020 17:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:00: Done! INFO @ Sun, 21 Jun 2020 17:49:00: 10000000 INFO @ Sun, 21 Jun 2020 17:49:00: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:49:00: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:49:00: #1 total tags in treatment: 10022761 INFO @ Sun, 21 Jun 2020 17:49:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (587 chroms): 1 millis pass2 - checking and writing primary data (2995 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:49:00: 5000000 INFO @ Sun, 21 Jun 2020 17:49:00: #1 tags after filtering in treatment: 10022673 INFO @ Sun, 21 Jun 2020 17:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:00: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:01: #2 number of paired peaks: 1898 INFO @ Sun, 21 Jun 2020 17:49:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:01: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:01: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:01: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:01: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 17:49:01: #2 alternative fragment length(s) may be 2,39,575 bps INFO @ Sun, 21 Jun 2020 17:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.10_model.r WARNING @ Sun, 21 Jun 2020 17:49:01: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:01: #2 You may need to consider one of the other alternative d(s): 2,39,575 WARNING @ Sun, 21 Jun 2020 17:49:01: #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 17:49:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:06: 6000000 INFO @ Sun, 21 Jun 2020 17:49:11: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:49:17: 8000000 INFO @ Sun, 21 Jun 2020 17:49:23: 9000000 INFO @ Sun, 21 Jun 2020 17:49:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:28: 10000000 INFO @ Sun, 21 Jun 2020 17:49:29: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:49:29: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:49:29: #1 total tags in treatment: 10022761 INFO @ Sun, 21 Jun 2020 17:49:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:29: #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 17:49:29: #1 tags after filtering in treatment: 10022673 INFO @ Sun, 21 Jun 2020 17:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:29: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:30: #2 number of paired peaks: 1898 INFO @ Sun, 21 Jun 2020 17:49:30: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:30: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 17:49:30: #2 alternative fragment length(s) may be 2,39,575 bps INFO @ Sun, 21 Jun 2020 17:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.20_model.r WARNING @ Sun, 21 Jun 2020 17:49:30: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:30: #2 You may need to consider one of the other alternative d(s): 2,39,575 WARNING @ Sun, 21 Jun 2020 17:49:30: #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 17:49:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.10_summits.bed INFO @ Sun, 21 Jun 2020 17:49:34: Done! pass1 - making usageList (475 chroms): 1 millis pass2 - checking and writing primary data (1725 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:49:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX149196/SRX149196.20_summits.bed INFO @ Sun, 21 Jun 2020 17:50:03: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (404 records, 4 fields): 6 millis CompletedMACS2peakCalling