Job ID = 6457206 SRX = SRX4563528 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:40:56 prefetch.2.10.7: 1) Downloading 'SRR7706255'... 2020-06-21T11:40:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:43:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:43:43 prefetch.2.10.7: 'SRR7706255' is valid 2020-06-21T11:43:43 prefetch.2.10.7: 1) 'SRR7706255' was downloaded successfully Read 14336771 spots for SRR7706255/SRR7706255.sra Written 14336771 spots for SRR7706255/SRR7706255.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: 00:03:35 14336771 reads; of these: 14336771 (100.00%) were unpaired; of these: 1124102 (7.84%) aligned 0 times 10432164 (72.77%) aligned exactly 1 time 2780505 (19.39%) aligned >1 times 92.16% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6286016 / 13212669 = 0.4758 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 20:51:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.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 20:51:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:23: 1000000 INFO @ Sun, 21 Jun 2020 20:51:29: 2000000 INFO @ Sun, 21 Jun 2020 20:51:34: 3000000 INFO @ Sun, 21 Jun 2020 20:51:40: 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 20:51:46: 5000000 INFO @ Sun, 21 Jun 2020 20:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.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 20:51:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:52: 6000000 INFO @ Sun, 21 Jun 2020 20:51:53: 1000000 INFO @ Sun, 21 Jun 2020 20:51:58: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:51:58: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:51:58: #1 total tags in treatment: 6926653 INFO @ Sun, 21 Jun 2020 20:51:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:58: #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 20:51:58: #1 tags after filtering in treatment: 6926521 INFO @ Sun, 21 Jun 2020 20:51:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:59: #2 number of paired peaks: 3129 INFO @ Sun, 21 Jun 2020 20:51:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:59: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 20:51:59: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 20:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.05_model.r INFO @ Sun, 21 Jun 2020 20:51:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:51:59: 2000000 INFO @ Sun, 21 Jun 2020 20:52:05: 3000000 INFO @ Sun, 21 Jun 2020 20:52:10: 4000000 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 20:52:16: 5000000 INFO @ Sun, 21 Jun 2020 20:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.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 20:52:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:52:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:52:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:22: 6000000 INFO @ Sun, 21 Jun 2020 20:52:23: 1000000 INFO @ Sun, 21 Jun 2020 20:52:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.05_summits.bed INFO @ Sun, 21 Jun 2020 20:52:26: Done! pass1 - making usageList (580 chroms): 2 millis pass2 - checking and writing primary data (4682 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:52:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:52:27: #1 total tags in treatment: 6926653 INFO @ Sun, 21 Jun 2020 20:52:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:27: #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 20:52:28: #1 tags after filtering in treatment: 6926521 INFO @ Sun, 21 Jun 2020 20:52:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:28: #2 number of paired peaks: 3129 INFO @ Sun, 21 Jun 2020 20:52:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:28: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 20:52:28: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 20:52:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.10_model.r INFO @ Sun, 21 Jun 2020 20:52:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:52:29: 2000000 INFO @ Sun, 21 Jun 2020 20:52:34: 3000000 INFO @ Sun, 21 Jun 2020 20:52:40: 4000000 INFO @ Sun, 21 Jun 2020 20:52:46: 5000000 INFO @ Sun, 21 Jun 2020 20:52:47: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:52:52: 6000000 INFO @ Sun, 21 Jun 2020 20:52:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.10_summits.bed INFO @ Sun, 21 Jun 2020 20:52:55: Done! pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (3206 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:57: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:52:57: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:52:57: #1 total tags in treatment: 6926653 INFO @ Sun, 21 Jun 2020 20:52:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:57: #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 20:52:58: #1 tags after filtering in treatment: 6926521 INFO @ Sun, 21 Jun 2020 20:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:58: #2 number of paired peaks: 3129 INFO @ Sun, 21 Jun 2020 20:52:58: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:59: #2 predicted fragment length is 232 bps INFO @ Sun, 21 Jun 2020 20:52:59: #2 alternative fragment length(s) may be 232 bps INFO @ Sun, 21 Jun 2020 20:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.20_model.r INFO @ Sun, 21 Jun 2020 20:52:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:53:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:53:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:53:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:53:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563528/SRX4563528.20_summits.bed INFO @ Sun, 21 Jun 2020 20:53:26: Done! pass1 - making usageList (176 chroms): 1 millis pass2 - checking and writing primary data (1948 records, 4 fields): 8 millis CompletedMACS2peakCalling