Job ID = 6454288 SRX = SRX197562 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:03:35 prefetch.2.10.7: 1) Downloading 'SRR596990'... 2020-06-21T09:03:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:04:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:04:20 prefetch.2.10.7: 'SRR596990' is valid 2020-06-21T09:04:20 prefetch.2.10.7: 1) 'SRR596990' was downloaded successfully Read 4040941 spots for SRR596990/SRR596990.sra Written 4040941 spots for SRR596990/SRR596990.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: 00:00:50 4040941 reads; of these: 4040941 (100.00%) were unpaired; of these: 705958 (17.47%) aligned 0 times 2596334 (64.25%) aligned exactly 1 time 738649 (18.28%) aligned >1 times 82.53% overall alignment rate Time searching: 00:00:50 Overall time: 00:00:50 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] 213894 / 3334983 = 0.0641 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 18:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.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 18:06:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:50: 1000000 INFO @ Sun, 21 Jun 2020 18:06:57: 2000000 INFO @ Sun, 21 Jun 2020 18:07:05: 3000000 INFO @ Sun, 21 Jun 2020 18:07:06: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:07:06: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:07:06: #1 total tags in treatment: 3121089 INFO @ Sun, 21 Jun 2020 18:07:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:06: #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 18:07:06: #1 tags after filtering in treatment: 3121043 INFO @ Sun, 21 Jun 2020 18:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:06: #2 number of paired peaks: 1564 INFO @ Sun, 21 Jun 2020 18:07:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:06: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:07:06: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 18:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.05_model.r INFO @ Sun, 21 Jun 2020 18:07:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:06: #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 18:07:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.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 18:07:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:19: 1000000 INFO @ Sun, 21 Jun 2020 18:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.05_summits.bed INFO @ Sun, 21 Jun 2020 18:07:19: Done! pass1 - making usageList (276 chroms): 1 millis pass2 - checking and writing primary data (2639 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:24: 2000000 INFO @ Sun, 21 Jun 2020 18:07:30: 3000000 INFO @ Sun, 21 Jun 2020 18:07:31: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:07:31: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:07:31: #1 total tags in treatment: 3121089 INFO @ Sun, 21 Jun 2020 18:07:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:31: #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 18:07:32: #1 tags after filtering in treatment: 3121043 INFO @ Sun, 21 Jun 2020 18:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:32: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:32: #2 number of paired peaks: 1564 INFO @ Sun, 21 Jun 2020 18:07:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:32: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:07:32: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 18:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.10_model.r INFO @ Sun, 21 Jun 2020 18:07:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:39: #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 18:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.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 18:07:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.10_summits.bed INFO @ Sun, 21 Jun 2020 18:07:43: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (1296 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:49: 1000000 INFO @ Sun, 21 Jun 2020 18:07:54: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:08:00: 3000000 INFO @ Sun, 21 Jun 2020 18:08:01: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 18:08:01: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 18:08:01: #1 total tags in treatment: 3121089 INFO @ Sun, 21 Jun 2020 18:08:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:01: #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 18:08:01: #1 tags after filtering in treatment: 3121043 INFO @ Sun, 21 Jun 2020 18:08:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:02: #2 number of paired peaks: 1564 INFO @ Sun, 21 Jun 2020 18:08:02: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:02: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:02: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 18:08:02: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 18:08:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.20_model.r INFO @ Sun, 21 Jun 2020 18:08:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:08:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX197562/SRX197562.20_summits.bed INFO @ Sun, 21 Jun 2020 18:08:14: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 26 millis CompletedMACS2peakCalling