Job ID = 6454135 SRX = SRX183881 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:51:04 prefetch.2.10.7: 1) Downloading 'SRR557676'... 2020-06-21T08:51:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:50 prefetch.2.10.7: 'SRR557676' is valid 2020-06-21T08:51:50 prefetch.2.10.7: 1) 'SRR557676' was downloaded successfully Read 6924965 spots for SRR557676/SRR557676.sra Written 6924965 spots for SRR557676/SRR557676.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: 00:01:12 6924965 reads; of these: 6924965 (100.00%) were unpaired; of these: 517544 (7.47%) aligned 0 times 5421476 (78.29%) aligned exactly 1 time 985945 (14.24%) aligned >1 times 92.53% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 910733 / 6407421 = 0.1421 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 17:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.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 17:55:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:14: 1000000 INFO @ Sun, 21 Jun 2020 17:55:20: 2000000 INFO @ Sun, 21 Jun 2020 17:55:25: 3000000 INFO @ Sun, 21 Jun 2020 17:55:31: 4000000 INFO @ Sun, 21 Jun 2020 17:55:37: 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 17:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.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 17:55:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:55:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:55:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:55:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:55:40: #1 total tags in treatment: 5496688 INFO @ Sun, 21 Jun 2020 17:55:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:40: #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 17:55:40: #1 tags after filtering in treatment: 5496562 INFO @ Sun, 21 Jun 2020 17:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:55:41: #2 number of paired peaks: 2135 INFO @ Sun, 21 Jun 2020 17:55:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:41: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 17:55:41: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 17:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.05_model.r INFO @ Sun, 21 Jun 2020 17:55:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:44: 1000000 INFO @ Sun, 21 Jun 2020 17:55:50: 2000000 INFO @ Sun, 21 Jun 2020 17:55:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:55: 3000000 INFO @ Sun, 21 Jun 2020 17:55:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.05_summits.bed INFO @ Sun, 21 Jun 2020 17:56:00: Done! pass1 - making usageList (277 chroms): 2 millis pass2 - checking and writing primary data (9365 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:56:01: 4000000 INFO @ Sun, 21 Jun 2020 17:56:07: 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 17:56:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.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 17:56:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:10: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:56:10: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:56:10: #1 total tags in treatment: 5496688 INFO @ Sun, 21 Jun 2020 17:56:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:10: #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 17:56:10: #1 tags after filtering in treatment: 5496562 INFO @ Sun, 21 Jun 2020 17:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:11: #2 number of paired peaks: 2135 INFO @ Sun, 21 Jun 2020 17:56:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:11: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 17:56:11: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 17:56:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.10_model.r INFO @ Sun, 21 Jun 2020 17:56:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:56:14: 1000000 INFO @ Sun, 21 Jun 2020 17:56:20: 2000000 INFO @ Sun, 21 Jun 2020 17:56:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:56:25: 3000000 INFO @ Sun, 21 Jun 2020 17:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.10_summits.bed INFO @ Sun, 21 Jun 2020 17:56:30: Done! pass1 - making usageList (185 chroms): 2 millis pass2 - checking and writing primary data (5078 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:56:31: 4000000 INFO @ Sun, 21 Jun 2020 17:56:37: 5000000 INFO @ Sun, 21 Jun 2020 17:56:40: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:56:40: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:56:40: #1 total tags in treatment: 5496688 INFO @ Sun, 21 Jun 2020 17:56:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:56:40: #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 17:56:40: #1 tags after filtering in treatment: 5496562 INFO @ Sun, 21 Jun 2020 17:56:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:56:40: #1 finished! INFO @ Sun, 21 Jun 2020 17:56:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:56:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:56:41: #2 number of paired peaks: 2135 INFO @ Sun, 21 Jun 2020 17:56:41: start model_add_line... INFO @ Sun, 21 Jun 2020 17:56:41: start X-correlation... INFO @ Sun, 21 Jun 2020 17:56:41: end of X-cor INFO @ Sun, 21 Jun 2020 17:56:41: #2 finished! INFO @ Sun, 21 Jun 2020 17:56:41: #2 predicted fragment length is 99 bps INFO @ Sun, 21 Jun 2020 17:56:41: #2 alternative fragment length(s) may be 99 bps INFO @ Sun, 21 Jun 2020 17:56:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.20_model.r INFO @ Sun, 21 Jun 2020 17:56:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:56:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:56:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183881/SRX183881.20_summits.bed INFO @ Sun, 21 Jun 2020 17:57:00: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (2500 records, 4 fields): 7 millis CompletedMACS2peakCalling