Job ID = 6457857 SRX = SRX481093 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:01:32 prefetch.2.10.7: 1) Downloading 'SRR1182704'... 2020-06-21T12:01:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:04:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:04:20 prefetch.2.10.7: 'SRR1182704' is valid 2020-06-21T12:04:20 prefetch.2.10.7: 1) 'SRR1182704' was downloaded successfully Read 13900069 spots for SRR1182704/SRR1182704.sra Written 13900069 spots for SRR1182704/SRR1182704.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: 00:03:24 13900069 reads; of these: 13900069 (100.00%) were unpaired; of these: 608232 (4.38%) aligned 0 times 11487780 (82.65%) aligned exactly 1 time 1804057 (12.98%) aligned >1 times 95.62% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 4093609 / 13291837 = 0.3080 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 21:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.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 21:12:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:06: 1000000 INFO @ Sun, 21 Jun 2020 21:12:11: 2000000 INFO @ Sun, 21 Jun 2020 21:12:16: 3000000 INFO @ Sun, 21 Jun 2020 21:12:21: 4000000 INFO @ Sun, 21 Jun 2020 21:12:26: 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 21:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.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 21:12:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:31: 6000000 INFO @ Sun, 21 Jun 2020 21:12:36: 1000000 INFO @ Sun, 21 Jun 2020 21:12:37: 7000000 INFO @ Sun, 21 Jun 2020 21:12:41: 2000000 INFO @ Sun, 21 Jun 2020 21:12:42: 8000000 INFO @ Sun, 21 Jun 2020 21:12:46: 3000000 INFO @ Sun, 21 Jun 2020 21:12:48: 9000000 INFO @ Sun, 21 Jun 2020 21:12:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:12:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:12:49: #1 total tags in treatment: 9198228 INFO @ Sun, 21 Jun 2020 21:12:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:12:49: #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 21:12:49: #1 tags after filtering in treatment: 9198221 INFO @ Sun, 21 Jun 2020 21:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:12:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:12:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:12:51: #2 number of paired peaks: 9457 INFO @ Sun, 21 Jun 2020 21:12:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:12:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:12:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:12:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:12:51: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 21:12:51: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 21 Jun 2020 21:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.05_model.r INFO @ Sun, 21 Jun 2020 21:12:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:12:51: 4000000 INFO @ Sun, 21 Jun 2020 21:12:57: 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 21:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.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 21:13:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:13:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:13:02: 6000000 INFO @ Sun, 21 Jun 2020 21:13:05: 1000000 INFO @ Sun, 21 Jun 2020 21:13:07: 7000000 INFO @ Sun, 21 Jun 2020 21:13:11: 2000000 INFO @ Sun, 21 Jun 2020 21:13:13: 8000000 INFO @ Sun, 21 Jun 2020 21:13:16: 3000000 INFO @ Sun, 21 Jun 2020 21:13:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:18: 9000000 INFO @ Sun, 21 Jun 2020 21:13:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:13:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:13:20: #1 total tags in treatment: 9198228 INFO @ Sun, 21 Jun 2020 21:13:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:20: #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 21:13:20: #1 tags after filtering in treatment: 9198221 INFO @ Sun, 21 Jun 2020 21:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:20: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:21: 4000000 INFO @ Sun, 21 Jun 2020 21:13:21: #2 number of paired peaks: 9457 INFO @ Sun, 21 Jun 2020 21:13:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:21: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 21:13:21: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 21 Jun 2020 21:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.10_model.r INFO @ Sun, 21 Jun 2020 21:13:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:13:26: 5000000 INFO @ Sun, 21 Jun 2020 21:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.05_summits.bed INFO @ Sun, 21 Jun 2020 21:13:31: Done! INFO @ Sun, 21 Jun 2020 21:13:32: 6000000 pass1 - making usageList (441 chroms): 3 millis pass2 - checking and writing primary data (8323 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:13:37: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:13:42: 8000000 INFO @ Sun, 21 Jun 2020 21:13:47: 9000000 INFO @ Sun, 21 Jun 2020 21:13:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:13:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:13:49: #1 total tags in treatment: 9198228 INFO @ Sun, 21 Jun 2020 21:13:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:49: #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 21:13:49: #1 tags after filtering in treatment: 9198221 INFO @ Sun, 21 Jun 2020 21:13:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:51: #2 number of paired peaks: 9457 INFO @ Sun, 21 Jun 2020 21:13:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:51: #2 predicted fragment length is 192 bps INFO @ Sun, 21 Jun 2020 21:13:51: #2 alternative fragment length(s) may be 192 bps INFO @ Sun, 21 Jun 2020 21:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.20_model.r INFO @ Sun, 21 Jun 2020 21:13:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.10_summits.bed INFO @ Sun, 21 Jun 2020 21:14:02: Done! pass1 - making usageList (345 chroms): 2 millis pass2 - checking and writing primary data (7344 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:14:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX481093/SRX481093.20_summits.bed INFO @ Sun, 21 Jun 2020 21:14:30: Done! pass1 - making usageList (171 chroms): 2 millis pass2 - checking and writing primary data (5850 records, 4 fields): 12 millis CompletedMACS2peakCalling