Job ID = 6452945 SRX = SRX050608 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:01:54 prefetch.2.10.7: 1) Downloading 'SRR139090'... 2020-06-21T08:01:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:34 prefetch.2.10.7: 'SRR139090' is valid 2020-06-21T08:06:34 prefetch.2.10.7: 1) 'SRR139090' was downloaded successfully Read 22573162 spots for SRR139090/SRR139090.sra Written 22573162 spots for SRR139090/SRR139090.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: 00:03:32 22573162 reads; of these: 22573162 (100.00%) were unpaired; of these: 6044683 (26.78%) aligned 0 times 14977552 (66.35%) aligned exactly 1 time 1550927 (6.87%) aligned >1 times 73.22% overall alignment rate Time searching: 00:03:33 Overall time: 00:03:33 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] 6982804 / 16528479 = 0.4225 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 17:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.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 17:14:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:21: 1000000 INFO @ Sun, 21 Jun 2020 17:14:27: 2000000 INFO @ Sun, 21 Jun 2020 17:14:32: 3000000 INFO @ Sun, 21 Jun 2020 17:14:37: 4000000 INFO @ Sun, 21 Jun 2020 17:14:42: 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 17:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.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 17:14:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:14:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:14:48: 6000000 INFO @ Sun, 21 Jun 2020 17:14:51: 1000000 INFO @ Sun, 21 Jun 2020 17:14:54: 7000000 INFO @ Sun, 21 Jun 2020 17:14:57: 2000000 INFO @ Sun, 21 Jun 2020 17:15:00: 8000000 INFO @ Sun, 21 Jun 2020 17:15:02: 3000000 INFO @ Sun, 21 Jun 2020 17:15:05: 9000000 INFO @ Sun, 21 Jun 2020 17:15:07: 4000000 INFO @ Sun, 21 Jun 2020 17:15:08: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:15:08: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:15:08: #1 total tags in treatment: 9545675 INFO @ Sun, 21 Jun 2020 17:15:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:08: #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 17:15:09: #1 tags after filtering in treatment: 9545504 INFO @ Sun, 21 Jun 2020 17:15:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:09: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:10: #2 number of paired peaks: 1575 INFO @ Sun, 21 Jun 2020 17:15:10: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:10: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:10: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:10: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:10: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 17:15:10: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 17:15:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.05_model.r INFO @ Sun, 21 Jun 2020 17:15:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:15:12: 5000000 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 17:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.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 17:15:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:15:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:15:16: 6000000 INFO @ Sun, 21 Jun 2020 17:15:20: 1000000 INFO @ Sun, 21 Jun 2020 17:15:21: 7000000 INFO @ Sun, 21 Jun 2020 17:15:25: 2000000 INFO @ Sun, 21 Jun 2020 17:15:27: 8000000 INFO @ Sun, 21 Jun 2020 17:15:30: 3000000 INFO @ Sun, 21 Jun 2020 17:15:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:15:32: 9000000 INFO @ Sun, 21 Jun 2020 17:15:34: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:15:34: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:15:34: #1 total tags in treatment: 9545675 INFO @ Sun, 21 Jun 2020 17:15:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:15:34: #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 17:15:35: #1 tags after filtering in treatment: 9545504 INFO @ Sun, 21 Jun 2020 17:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:15:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:15:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:15:35: 4000000 INFO @ Sun, 21 Jun 2020 17:15:36: #2 number of paired peaks: 1575 INFO @ Sun, 21 Jun 2020 17:15:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:15:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:15:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:15:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:15:36: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 17:15:36: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 17:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.10_model.r INFO @ Sun, 21 Jun 2020 17:15:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:15:40: 5000000 INFO @ Sun, 21 Jun 2020 17:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.05_summits.bed INFO @ Sun, 21 Jun 2020 17:15:41: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (7127 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:15:45: 6000000 INFO @ Sun, 21 Jun 2020 17:15:49: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:15:55: 8000000 INFO @ Sun, 21 Jun 2020 17:15:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:15:59: 9000000 INFO @ Sun, 21 Jun 2020 17:16:02: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:16:02: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:16:02: #1 total tags in treatment: 9545675 INFO @ Sun, 21 Jun 2020 17:16:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:16:02: #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 17:16:02: #1 tags after filtering in treatment: 9545504 INFO @ Sun, 21 Jun 2020 17:16:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:16:02: #1 finished! INFO @ Sun, 21 Jun 2020 17:16:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:16:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:16:03: #2 number of paired peaks: 1575 INFO @ Sun, 21 Jun 2020 17:16:03: start model_add_line... INFO @ Sun, 21 Jun 2020 17:16:03: start X-correlation... INFO @ Sun, 21 Jun 2020 17:16:03: end of X-cor INFO @ Sun, 21 Jun 2020 17:16:03: #2 finished! INFO @ Sun, 21 Jun 2020 17:16:03: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 17:16:03: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 17:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.20_model.r INFO @ Sun, 21 Jun 2020 17:16:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:16:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.10_summits.bed INFO @ Sun, 21 Jun 2020 17:16:08: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (4616 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:16:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:16:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:16:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:16:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050608/SRX050608.20_summits.bed INFO @ Sun, 21 Jun 2020 17:16:35: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (2387 records, 4 fields): 4 millis CompletedMACS2peakCalling