Job ID = 6455923 SRX = SRX3068962 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:07 prefetch.2.10.7: 1) Downloading 'SRR5907438'... 2020-06-21T10:16:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:34 prefetch.2.10.7: 'SRR5907438' is valid 2020-06-21T10:18:34 prefetch.2.10.7: 1) 'SRR5907438' was downloaded successfully Read 13431315 spots for SRR5907438/SRR5907438.sra Written 13431315 spots for SRR5907438/SRR5907438.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: 00:02:47 13431315 reads; of these: 13431315 (100.00%) were unpaired; of these: 3198978 (23.82%) aligned 0 times 8585506 (63.92%) aligned exactly 1 time 1646831 (12.26%) aligned >1 times 76.18% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 3910677 / 10232337 = 0.3822 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 19:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.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 19:24:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:24:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:24:56: 1000000 INFO @ Sun, 21 Jun 2020 19:25:02: 2000000 INFO @ Sun, 21 Jun 2020 19:25:09: 3000000 INFO @ Sun, 21 Jun 2020 19:25:15: 4000000 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 19:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.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 19:25:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:21: 5000000 INFO @ Sun, 21 Jun 2020 19:25:26: 1000000 INFO @ Sun, 21 Jun 2020 19:25:29: 6000000 INFO @ Sun, 21 Jun 2020 19:25:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:25:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:25:31: #1 total tags in treatment: 6321660 INFO @ Sun, 21 Jun 2020 19:25:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:31: #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 19:25:31: #1 tags after filtering in treatment: 6321636 INFO @ Sun, 21 Jun 2020 19:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:32: #2 number of paired peaks: 1327 INFO @ Sun, 21 Jun 2020 19:25:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:32: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:32: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:32: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:32: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:25:32: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 19:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.05_model.r INFO @ Sun, 21 Jun 2020 19:25:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:32: 2000000 INFO @ Sun, 21 Jun 2020 19:25:38: 3000000 INFO @ Sun, 21 Jun 2020 19:25:44: 4000000 INFO @ Sun, 21 Jun 2020 19:25:47: #3 Call peaks for each chromosome... 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 19:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.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 19:25:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:50: 5000000 INFO @ Sun, 21 Jun 2020 19:25:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.05_summits.bed INFO @ Sun, 21 Jun 2020 19:25:55: Done! pass1 - making usageList (506 chroms): 2 millis pass2 - checking and writing primary data (5637 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:25:57: 1000000 INFO @ Sun, 21 Jun 2020 19:25:57: 6000000 INFO @ Sun, 21 Jun 2020 19:25:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:25:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:25:59: #1 total tags in treatment: 6321660 INFO @ Sun, 21 Jun 2020 19:25:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:59: #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 19:26:00: #1 tags after filtering in treatment: 6321636 INFO @ Sun, 21 Jun 2020 19:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:00: #2 number of paired peaks: 1327 INFO @ Sun, 21 Jun 2020 19:26:00: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:00: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:00: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:00: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:00: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:26:00: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 19:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.10_model.r INFO @ Sun, 21 Jun 2020 19:26:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:03: 2000000 INFO @ Sun, 21 Jun 2020 19:26:10: 3000000 INFO @ Sun, 21 Jun 2020 19:26:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:26:23: 5000000 INFO @ Sun, 21 Jun 2020 19:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.10_summits.bed INFO @ Sun, 21 Jun 2020 19:26:24: Done! pass1 - making usageList (426 chroms): 2 millis pass2 - checking and writing primary data (2967 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:26:29: 6000000 INFO @ Sun, 21 Jun 2020 19:26:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:26:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:26:32: #1 total tags in treatment: 6321660 INFO @ Sun, 21 Jun 2020 19:26:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:32: #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 19:26:32: #1 tags after filtering in treatment: 6321636 INFO @ Sun, 21 Jun 2020 19:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:33: #2 number of paired peaks: 1327 INFO @ Sun, 21 Jun 2020 19:26:33: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:33: #2 predicted fragment length is 140 bps INFO @ Sun, 21 Jun 2020 19:26:33: #2 alternative fragment length(s) may be 140 bps INFO @ Sun, 21 Jun 2020 19:26:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.20_model.r INFO @ Sun, 21 Jun 2020 19:26:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:26:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3068962/SRX3068962.20_summits.bed INFO @ Sun, 21 Jun 2020 19:26:56: Done! pass1 - making usageList (311 chroms): 1 millis pass2 - checking and writing primary data (1336 records, 4 fields): 12 millis CompletedMACS2peakCalling