Job ID = 6454294 SRX = SRX197568 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:14:09 prefetch.2.10.7: 1) Downloading 'SRR596996'... 2020-06-21T09:14:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:17:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:17:50 prefetch.2.10.7: 1) 'SRR596996' was downloaded successfully Read 28671012 spots for SRR596996/SRR596996.sra Written 28671012 spots for SRR596996/SRR596996.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: 00:00:01 Multiseed full-index search: 00:06:55 28671012 reads; of these: 28671012 (100.00%) were unpaired; of these: 2785063 (9.71%) aligned 0 times 18076892 (63.05%) aligned exactly 1 time 7809057 (27.24%) aligned >1 times 90.29% overall alignment rate Time searching: 00:06:56 Overall time: 00:06:56 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10127181 / 25885949 = 0.3912 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 18:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.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 18:31:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:37: 1000000 INFO @ Sun, 21 Jun 2020 18:31:42: 2000000 INFO @ Sun, 21 Jun 2020 18:31:47: 3000000 INFO @ Sun, 21 Jun 2020 18:31:51: 4000000 INFO @ Sun, 21 Jun 2020 18:31:56: 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 18:32:01: 6000000 INFO @ Sun, 21 Jun 2020 18:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.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 18:32:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:06: 7000000 INFO @ Sun, 21 Jun 2020 18:32:08: 1000000 INFO @ Sun, 21 Jun 2020 18:32:12: 8000000 INFO @ Sun, 21 Jun 2020 18:32:14: 2000000 INFO @ Sun, 21 Jun 2020 18:32:17: 9000000 INFO @ Sun, 21 Jun 2020 18:32:20: 3000000 INFO @ Sun, 21 Jun 2020 18:32:23: 10000000 INFO @ Sun, 21 Jun 2020 18:32:27: 4000000 INFO @ Sun, 21 Jun 2020 18:32:28: 11000000 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 18:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.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 18:32:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:33: 5000000 INFO @ Sun, 21 Jun 2020 18:32:33: 12000000 INFO @ Sun, 21 Jun 2020 18:32:38: 1000000 INFO @ Sun, 21 Jun 2020 18:32:39: 6000000 INFO @ Sun, 21 Jun 2020 18:32:39: 13000000 INFO @ Sun, 21 Jun 2020 18:32:43: 2000000 INFO @ Sun, 21 Jun 2020 18:32:45: 14000000 INFO @ Sun, 21 Jun 2020 18:32:45: 7000000 INFO @ Sun, 21 Jun 2020 18:32:49: 3000000 INFO @ Sun, 21 Jun 2020 18:32:50: 15000000 INFO @ Sun, 21 Jun 2020 18:32:52: 8000000 INFO @ Sun, 21 Jun 2020 18:32:54: 4000000 INFO @ Sun, 21 Jun 2020 18:32:55: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:32:55: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:32:55: #1 total tags in treatment: 15758768 INFO @ Sun, 21 Jun 2020 18:32:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:55: #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 18:32:55: #1 tags after filtering in treatment: 15758768 INFO @ Sun, 21 Jun 2020 18:32:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:57: #2 number of paired peaks: 1232 INFO @ Sun, 21 Jun 2020 18:32:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:57: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:32:57: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 18:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.05_model.r WARNING @ Sun, 21 Jun 2020 18:32:57: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:57: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 18:32:57: #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 18:32:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:58: 9000000 INFO @ Sun, 21 Jun 2020 18:33:00: 5000000 INFO @ Sun, 21 Jun 2020 18:33:04: 10000000 INFO @ Sun, 21 Jun 2020 18:33:06: 6000000 INFO @ Sun, 21 Jun 2020 18:33:10: 11000000 INFO @ Sun, 21 Jun 2020 18:33:11: 7000000 INFO @ Sun, 21 Jun 2020 18:33:16: 12000000 INFO @ Sun, 21 Jun 2020 18:33:17: 8000000 INFO @ Sun, 21 Jun 2020 18:33:22: 9000000 INFO @ Sun, 21 Jun 2020 18:33:23: 13000000 INFO @ Sun, 21 Jun 2020 18:33:28: 10000000 INFO @ Sun, 21 Jun 2020 18:33:29: 14000000 INFO @ Sun, 21 Jun 2020 18:33:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:33: 11000000 INFO @ Sun, 21 Jun 2020 18:33:35: 15000000 INFO @ Sun, 21 Jun 2020 18:33:39: 12000000 INFO @ Sun, 21 Jun 2020 18:33:40: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:33:40: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:33:40: #1 total tags in treatment: 15758768 INFO @ Sun, 21 Jun 2020 18:33:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:40: #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 18:33:41: #1 tags after filtering in treatment: 15758768 INFO @ Sun, 21 Jun 2020 18:33:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:41: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:42: #2 number of paired peaks: 1232 INFO @ Sun, 21 Jun 2020 18:33:42: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:42: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:42: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:42: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:42: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:33:42: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 18:33:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.10_model.r WARNING @ Sun, 21 Jun 2020 18:33:42: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:42: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 18:33:42: #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 18:33:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:45: 13000000 INFO @ Sun, 21 Jun 2020 18:33:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.05_summits.bed INFO @ Sun, 21 Jun 2020 18:33:47: Done! pass1 - making usageList (737 chroms): 1 millis pass2 - checking and writing primary data (5697 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:50: 14000000 INFO @ Sun, 21 Jun 2020 18:33:55: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:34:00: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:34:00: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:34:00: #1 total tags in treatment: 15758768 INFO @ Sun, 21 Jun 2020 18:34:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:00: #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 18:34:00: #1 tags after filtering in treatment: 15758768 INFO @ Sun, 21 Jun 2020 18:34:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:01: #2 number of paired peaks: 1232 INFO @ Sun, 21 Jun 2020 18:34:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:02: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:02: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 18:34:02: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 18:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.20_model.r WARNING @ Sun, 21 Jun 2020 18:34:02: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:02: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 18:34:02: #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 18:34:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:34: Done! pass1 - making usageList (603 chroms): 2 millis pass2 - checking and writing primary data (4103 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:34:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197568/SRX197568.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:54: Done! pass1 - making usageList (417 chroms): 1 millis pass2 - checking and writing primary data (2541 records, 4 fields): 16 millis CompletedMACS2peakCalling