Job ID = 6457240 SRX = SRX4579160 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:36:44 prefetch.2.10.7: 1) Downloading 'SRR7722303'... 2020-06-21T11:36:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:42:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:42:30 prefetch.2.10.7: 1) 'SRR7722303' was downloaded successfully 2020-06-21T11:42:30 prefetch.2.10.7: 'SRR7722303' has 0 unresolved dependencies Read 51386187 spots for SRR7722303/SRR7722303.sra Written 51386187 spots for SRR7722303/SRR7722303.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: 00:06:20 51386187 reads; of these: 51386187 (100.00%) were unpaired; of these: 46437260 (90.37%) aligned 0 times 3910169 (7.61%) aligned exactly 1 time 1038758 (2.02%) aligned >1 times 9.63% overall alignment rate Time searching: 00:06:20 Overall time: 00:06:20 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] 678928 / 4948927 = 0.1372 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 20:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.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 20:53:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:53:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:53:20: 1000000 INFO @ Sun, 21 Jun 2020 20:53:26: 2000000 INFO @ Sun, 21 Jun 2020 20:53:31: 3000000 INFO @ Sun, 21 Jun 2020 20:53:36: 4000000 INFO @ Sun, 21 Jun 2020 20:53:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:53:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:53:38: #1 total tags in treatment: 4269999 INFO @ Sun, 21 Jun 2020 20:53:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:53:38: #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 20:53:38: #1 tags after filtering in treatment: 4269633 INFO @ Sun, 21 Jun 2020 20:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:53:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:53:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:53:39: #2 number of paired peaks: 7318 INFO @ Sun, 21 Jun 2020 20:53:39: start model_add_line... INFO @ Sun, 21 Jun 2020 20:53:39: start X-correlation... INFO @ Sun, 21 Jun 2020 20:53:39: end of X-cor INFO @ Sun, 21 Jun 2020 20:53:39: #2 finished! INFO @ Sun, 21 Jun 2020 20:53:39: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 20:53:39: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 20:53:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.05_model.r INFO @ Sun, 21 Jun 2020 20:53:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:53:39: #3 Pre-compute pvalue-qvalue table... 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 20:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.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 20:53:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:53:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:53:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:53:51: 1000000 INFO @ Sun, 21 Jun 2020 20:53:57: 2000000 INFO @ Sun, 21 Jun 2020 20:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.05_summits.bed INFO @ Sun, 21 Jun 2020 20:53:57: Done! pass1 - making usageList (191 chroms): 2 millis pass2 - checking and writing primary data (4980 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:54:02: 3000000 INFO @ Sun, 21 Jun 2020 20:54:08: 4000000 INFO @ Sun, 21 Jun 2020 20:54:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:54:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:54:10: #1 total tags in treatment: 4269999 INFO @ Sun, 21 Jun 2020 20:54:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:54:10: #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 20:54:10: #1 tags after filtering in treatment: 4269633 INFO @ Sun, 21 Jun 2020 20:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:54:10: #1 finished! INFO @ Sun, 21 Jun 2020 20:54:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:54:11: #2 number of paired peaks: 7318 INFO @ Sun, 21 Jun 2020 20:54:11: start model_add_line... INFO @ Sun, 21 Jun 2020 20:54:11: start X-correlation... INFO @ Sun, 21 Jun 2020 20:54:11: end of X-cor INFO @ Sun, 21 Jun 2020 20:54:11: #2 finished! INFO @ Sun, 21 Jun 2020 20:54:11: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 20:54:11: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 20:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.10_model.r INFO @ Sun, 21 Jun 2020 20:54:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:54:11: #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 20:54:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.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 20:54:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:54:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:54:21: 1000000 INFO @ Sun, 21 Jun 2020 20:54:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:54:26: 2000000 INFO @ Sun, 21 Jun 2020 20:54:31: 3000000 INFO @ Sun, 21 Jun 2020 20:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:54:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:54:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.10_summits.bed INFO @ Sun, 21 Jun 2020 20:54:31: Done! pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (1851 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:54:37: 4000000 INFO @ Sun, 21 Jun 2020 20:54:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:54:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:54:39: #1 total tags in treatment: 4269999 INFO @ Sun, 21 Jun 2020 20:54:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:54:39: #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 20:54:39: #1 tags after filtering in treatment: 4269633 INFO @ Sun, 21 Jun 2020 20:54:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:54:39: #1 finished! INFO @ Sun, 21 Jun 2020 20:54:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:54:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:54:40: #2 number of paired peaks: 7318 INFO @ Sun, 21 Jun 2020 20:54:40: start model_add_line... INFO @ Sun, 21 Jun 2020 20:54:40: start X-correlation... INFO @ Sun, 21 Jun 2020 20:54:40: end of X-cor INFO @ Sun, 21 Jun 2020 20:54:40: #2 finished! INFO @ Sun, 21 Jun 2020 20:54:40: #2 predicted fragment length is 213 bps INFO @ Sun, 21 Jun 2020 20:54:40: #2 alternative fragment length(s) may be 213 bps INFO @ Sun, 21 Jun 2020 20:54:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.20_model.r INFO @ Sun, 21 Jun 2020 20:54:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:54:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:54:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579160/SRX4579160.20_summits.bed INFO @ Sun, 21 Jun 2020 20:54:59: Done! pass1 - making usageList (92 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 5 millis CompletedMACS2peakCalling