Job ID = 6457210 SRX = SRX4563532 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:44:23 prefetch.2.10.7: 1) Downloading 'SRR7706259'... 2020-06-21T11:44:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:46:00 prefetch.2.10.7: 'SRR7706259' is valid 2020-06-21T11:46:00 prefetch.2.10.7: 1) 'SRR7706259' was downloaded successfully Read 5991739 spots for SRR7706259/SRR7706259.sra Written 5991739 spots for SRR7706259/SRR7706259.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: 00:01:31 5991739 reads; of these: 5991739 (100.00%) were unpaired; of these: 351442 (5.87%) aligned 0 times 4340060 (72.43%) aligned exactly 1 time 1300237 (21.70%) aligned >1 times 94.13% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 2825156 / 5640297 = 0.5009 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 20:49:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.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 20:49:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:49:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:49:38: 1000000 INFO @ Sun, 21 Jun 2020 20:49:43: 2000000 INFO @ Sun, 21 Jun 2020 20:49:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:49:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:49:47: #1 total tags in treatment: 2815141 INFO @ Sun, 21 Jun 2020 20:49:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:49:47: #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 20:49:48: #1 tags after filtering in treatment: 2814931 INFO @ Sun, 21 Jun 2020 20:49:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:49:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:49:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:49:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:49:48: #2 number of paired peaks: 2944 INFO @ Sun, 21 Jun 2020 20:49:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:49:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:49:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:49:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:49:48: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:49:48: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:49:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.05_model.r INFO @ Sun, 21 Jun 2020 20:49:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:49:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:49:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:49:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:49:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:49:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.05_summits.bed INFO @ Sun, 21 Jun 2020 20:49:59: Done! pass1 - making usageList (534 chroms): 2 millis pass2 - checking and writing primary data (2719 records, 4 fields): 15 millis CompletedMACS2peakCalling 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 20:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.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 20:50:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:08: 1000000 INFO @ Sun, 21 Jun 2020 20:50:13: 2000000 INFO @ Sun, 21 Jun 2020 20:50:18: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:50:18: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:50:18: #1 total tags in treatment: 2815141 INFO @ Sun, 21 Jun 2020 20:50:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:50:18: #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 20:50:18: #1 tags after filtering in treatment: 2814931 INFO @ Sun, 21 Jun 2020 20:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:50:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:50:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:50:18: #2 number of paired peaks: 2944 INFO @ Sun, 21 Jun 2020 20:50:18: start model_add_line... INFO @ Sun, 21 Jun 2020 20:50:18: start X-correlation... INFO @ Sun, 21 Jun 2020 20:50:18: end of X-cor INFO @ Sun, 21 Jun 2020 20:50:18: #2 finished! INFO @ Sun, 21 Jun 2020 20:50:18: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:50:18: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:50:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.10_model.r INFO @ Sun, 21 Jun 2020 20:50:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:50:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.10_summits.bed INFO @ Sun, 21 Jun 2020 20:50:29: Done! pass1 - making usageList (310 chroms): 1 millis pass2 - checking and writing primary data (1681 records, 4 fields): 11 millis CompletedMACS2peakCalling 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 20:50:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.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 20:50:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:50:38: 1000000 INFO @ Sun, 21 Jun 2020 20:50:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:50:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:50:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:50:48: #1 total tags in treatment: 2815141 INFO @ Sun, 21 Jun 2020 20:50:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:50:48: #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 20:50:48: #1 tags after filtering in treatment: 2814931 INFO @ Sun, 21 Jun 2020 20:50:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:50:48: #1 finished! INFO @ Sun, 21 Jun 2020 20:50:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:50:48: #2 number of paired peaks: 2944 INFO @ Sun, 21 Jun 2020 20:50:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:50:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:50:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:50:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:50:48: #2 predicted fragment length is 207 bps INFO @ Sun, 21 Jun 2020 20:50:48: #2 alternative fragment length(s) may be 207 bps INFO @ Sun, 21 Jun 2020 20:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.20_model.r INFO @ Sun, 21 Jun 2020 20:50:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:50:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:50:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563532/SRX4563532.20_summits.bed INFO @ Sun, 21 Jun 2020 20:51:00: Done! pass1 - making usageList (120 chroms): 1 millis pass2 - checking and writing primary data (926 records, 4 fields): 5 millis CompletedMACS2peakCalling