Job ID = 6456204 SRX = SRX330995 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:44:08 prefetch.2.10.7: 1) Downloading 'SRR947204'... 2020-06-21T10:44:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:44:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:44:20 prefetch.2.10.7: 'SRR947204' is valid 2020-06-21T10:44:20 prefetch.2.10.7: 1) 'SRR947204' was downloaded successfully Read 226496 spots for SRR947204/SRR947204.sra Written 226496 spots for SRR947204/SRR947204.sra 2020-06-21T10:44:32 prefetch.2.10.7: 1) Downloading 'SRR947205'... 2020-06-21T10:44:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:45:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:45:14 prefetch.2.10.7: 'SRR947205' is valid 2020-06-21T10:45:14 prefetch.2.10.7: 1) 'SRR947205' was downloaded successfully Read 6286532 spots for SRR947205/SRR947205.sra Written 6286532 spots for SRR947205/SRR947205.sra 2020-06-21T10:45:41 prefetch.2.10.7: 1) Downloading 'SRR947206'... 2020-06-21T10:45:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:45:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:45:58 prefetch.2.10.7: 'SRR947206' is valid 2020-06-21T10:45:58 prefetch.2.10.7: 1) 'SRR947206' was downloaded successfully Read 1188498 spots for SRR947206/SRR947206.sra Written 1188498 spots for SRR947206/SRR947206.sra 2020-06-21T10:46:12 prefetch.2.10.7: 1) Downloading 'SRR947207'... 2020-06-21T10:46:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:46:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:46:58 prefetch.2.10.7: 'SRR947207' is valid 2020-06-21T10:46:58 prefetch.2.10.7: 1) 'SRR947207' was downloaded successfully Read 3440887 spots for SRR947207/SRR947207.sra Written 3440887 spots for SRR947207/SRR947207.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: 00:01:54 11142413 reads; of these: 11142413 (100.00%) were unpaired; of these: 3298097 (29.60%) aligned 0 times 5659930 (50.80%) aligned exactly 1 time 2184386 (19.60%) aligned >1 times 70.40% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 2279094 / 7844316 = 0.2905 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 19:51:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.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 19:51:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:10: 1000000 INFO @ Sun, 21 Jun 2020 19:51:16: 2000000 INFO @ Sun, 21 Jun 2020 19:51:22: 3000000 INFO @ Sun, 21 Jun 2020 19:51:27: 4000000 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 19:51:33: 5000000 INFO @ Sun, 21 Jun 2020 19:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.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 19:51:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:37: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 19:51:37: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 19:51:37: #1 total tags in treatment: 5565222 INFO @ Sun, 21 Jun 2020 19:51:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:37: #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 19:51:37: #1 tags after filtering in treatment: 5565074 INFO @ Sun, 21 Jun 2020 19:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:38: #2 number of paired peaks: 5109 INFO @ Sun, 21 Jun 2020 19:51:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:38: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 19:51:38: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 19:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.05_model.r INFO @ Sun, 21 Jun 2020 19:51:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:40: 1000000 INFO @ Sun, 21 Jun 2020 19:51:45: 2000000 INFO @ Sun, 21 Jun 2020 19:51:50: 3000000 INFO @ Sun, 21 Jun 2020 19:51:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:55: 4000000 INFO @ Sun, 21 Jun 2020 19:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.05_summits.bed INFO @ Sun, 21 Jun 2020 19:51:57: Done! pass1 - making usageList (306 chroms): 3 millis pass2 - checking and writing primary data (12117 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:00: 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 19:52:03: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 19:52:03: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 19:52:03: #1 total tags in treatment: 5565222 INFO @ Sun, 21 Jun 2020 19:52:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:03: #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 19:52:04: #1 tags after filtering in treatment: 5565074 INFO @ Sun, 21 Jun 2020 19:52:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.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 19:52:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:04: #2 number of paired peaks: 5109 INFO @ Sun, 21 Jun 2020 19:52:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:04: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 19:52:04: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 19:52:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.10_model.r INFO @ Sun, 21 Jun 2020 19:52:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:52:10: 1000000 INFO @ Sun, 21 Jun 2020 19:52:16: 2000000 INFO @ Sun, 21 Jun 2020 19:52:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:22: 3000000 INFO @ Sun, 21 Jun 2020 19:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.10_summits.bed INFO @ Sun, 21 Jun 2020 19:52:24: Done! pass1 - making usageList (204 chroms): 2 millis pass2 - checking and writing primary data (7512 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:27: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:52:34: 5000000 INFO @ Sun, 21 Jun 2020 19:52:37: #1 tag size is determined as 33 bps INFO @ Sun, 21 Jun 2020 19:52:37: #1 tag size = 33 INFO @ Sun, 21 Jun 2020 19:52:37: #1 total tags in treatment: 5565222 INFO @ Sun, 21 Jun 2020 19:52:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:37: #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 19:52:37: #1 tags after filtering in treatment: 5565074 INFO @ Sun, 21 Jun 2020 19:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:38: #2 number of paired peaks: 5109 INFO @ Sun, 21 Jun 2020 19:52:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:38: #2 predicted fragment length is 82 bps INFO @ Sun, 21 Jun 2020 19:52:38: #2 alternative fragment length(s) may be 82 bps INFO @ Sun, 21 Jun 2020 19:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.20_model.r INFO @ Sun, 21 Jun 2020 19:52:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:52:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX330995/SRX330995.20_summits.bed INFO @ Sun, 21 Jun 2020 19:52:58: Done! pass1 - making usageList (157 chroms): 1 millis pass2 - checking and writing primary data (3766 records, 4 fields): 8 millis CompletedMACS2peakCalling