Job ID = 6457212 SRX = SRX4563534 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:36:25 prefetch.2.10.7: 1) Downloading 'SRR7706261'... 2020-06-21T11:36:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:38:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:38:01 prefetch.2.10.7: 'SRR7706261' is valid 2020-06-21T11:38:01 prefetch.2.10.7: 1) 'SRR7706261' was downloaded successfully Read 8708598 spots for SRR7706261/SRR7706261.sra Written 8708598 spots for SRR7706261/SRR7706261.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: 00:02:23 8708598 reads; of these: 8708598 (100.00%) were unpaired; of these: 539079 (6.19%) aligned 0 times 6163079 (70.77%) aligned exactly 1 time 2006440 (23.04%) aligned >1 times 93.81% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 5140937 / 8169519 = 0.6293 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 20:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.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 20:43:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:15: 1000000 INFO @ Sun, 21 Jun 2020 20:43:21: 2000000 INFO @ Sun, 21 Jun 2020 20:43:28: 3000000 INFO @ Sun, 21 Jun 2020 20:43:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:28: #1 total tags in treatment: 3028582 INFO @ Sun, 21 Jun 2020 20:43:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:28: #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 20:43:28: #1 tags after filtering in treatment: 3028432 INFO @ Sun, 21 Jun 2020 20:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:28: #2 number of paired peaks: 2876 INFO @ Sun, 21 Jun 2020 20:43:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:29: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 20:43:29: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 20:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.05_model.r INFO @ Sun, 21 Jun 2020 20:43:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:37: #3 Call peaks for each chromosome... 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 20:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.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 20:43:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.05_summits.bed INFO @ Sun, 21 Jun 2020 20:43:41: Done! pass1 - making usageList (678 chroms): 1 millis pass2 - checking and writing primary data (2313 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:46: 1000000 INFO @ Sun, 21 Jun 2020 20:43:51: 2000000 INFO @ Sun, 21 Jun 2020 20:43:58: 3000000 INFO @ Sun, 21 Jun 2020 20:43:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:58: #1 total tags in treatment: 3028582 INFO @ Sun, 21 Jun 2020 20:43:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:58: #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 20:43:58: #1 tags after filtering in treatment: 3028432 INFO @ Sun, 21 Jun 2020 20:43:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:59: #2 number of paired peaks: 2876 INFO @ Sun, 21 Jun 2020 20:43:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:59: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 20:43:59: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 20:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.10_model.r INFO @ Sun, 21 Jun 2020 20:43:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:44:07: #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 20:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.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 20:44:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:44:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.10_summits.bed INFO @ Sun, 21 Jun 2020 20:44:11: Done! pass1 - making usageList (504 chroms): 2 millis pass2 - checking and writing primary data (1352 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:16: 1000000 INFO @ Sun, 21 Jun 2020 20:44:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:44:30: 3000000 INFO @ Sun, 21 Jun 2020 20:44:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:44:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:44:30: #1 total tags in treatment: 3028582 INFO @ Sun, 21 Jun 2020 20:44:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:44:30: #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 20:44:30: #1 tags after filtering in treatment: 3028432 INFO @ Sun, 21 Jun 2020 20:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:44:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:44:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:44:30: #2 number of paired peaks: 2876 INFO @ Sun, 21 Jun 2020 20:44:30: start model_add_line... INFO @ Sun, 21 Jun 2020 20:44:30: start X-correlation... INFO @ Sun, 21 Jun 2020 20:44:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:44:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:44:31: #2 predicted fragment length is 174 bps INFO @ Sun, 21 Jun 2020 20:44:31: #2 alternative fragment length(s) may be 174 bps INFO @ Sun, 21 Jun 2020 20:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.20_model.r INFO @ Sun, 21 Jun 2020 20:44:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:44:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:44:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563534/SRX4563534.20_summits.bed INFO @ Sun, 21 Jun 2020 20:44:43: Done! pass1 - making usageList (220 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 8 millis CompletedMACS2peakCalling