Job ID = 6457207 SRX = SRX4563529 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:35:28 prefetch.2.10.7: 1) Downloading 'SRR7706256'... 2020-06-21T11:35:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:37:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:37:00 prefetch.2.10.7: 'SRR7706256' is valid 2020-06-21T11:37:00 prefetch.2.10.7: 1) 'SRR7706256' was downloaded successfully Read 9916105 spots for SRR7706256/SRR7706256.sra Written 9916105 spots for SRR7706256/SRR7706256.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: 00:02:17 9916105 reads; of these: 9916105 (100.00%) were unpaired; of these: 915277 (9.23%) aligned 0 times 8004147 (80.72%) aligned exactly 1 time 996681 (10.05%) aligned >1 times 90.77% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 5206240 / 9000828 = 0.5784 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 20:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.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 20:42:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:10: 1000000 INFO @ Sun, 21 Jun 2020 20:42:16: 2000000 INFO @ Sun, 21 Jun 2020 20:42:23: 3000000 INFO @ Sun, 21 Jun 2020 20:42:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:28: #1 total tags in treatment: 3794588 INFO @ Sun, 21 Jun 2020 20:42:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:28: #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 20:42:28: #1 tags after filtering in treatment: 3794335 INFO @ Sun, 21 Jun 2020 20:42:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:28: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:29: #2 number of paired peaks: 7069 INFO @ Sun, 21 Jun 2020 20:42:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:29: #2 predicted fragment length is 307 bps INFO @ Sun, 21 Jun 2020 20:42:29: #2 alternative fragment length(s) may be 307 bps INFO @ Sun, 21 Jun 2020 20:42:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.05_model.r INFO @ Sun, 21 Jun 2020 20:42:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:29: #3 Pre-compute pvalue-qvalue table... 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 20:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.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 20:42:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:39: 1000000 INFO @ Sun, 21 Jun 2020 20:42:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:44: 2000000 INFO @ Sun, 21 Jun 2020 20:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.05_summits.bed INFO @ Sun, 21 Jun 2020 20:42:45: Done! pass1 - making usageList (184 chroms): 1 millis pass2 - checking and writing primary data (7120 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:42:50: 3000000 INFO @ Sun, 21 Jun 2020 20:42:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:54: #1 total tags in treatment: 3794588 INFO @ Sun, 21 Jun 2020 20:42:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:54: #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 20:42:55: #1 tags after filtering in treatment: 3794335 INFO @ Sun, 21 Jun 2020 20:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:55: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:55: #2 number of paired peaks: 7069 INFO @ Sun, 21 Jun 2020 20:42:55: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:55: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:55: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:55: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:55: #2 predicted fragment length is 307 bps INFO @ Sun, 21 Jun 2020 20:42:55: #2 alternative fragment length(s) may be 307 bps INFO @ Sun, 21 Jun 2020 20:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.10_model.r INFO @ Sun, 21 Jun 2020 20:42:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:55: #3 Pre-compute pvalue-qvalue table... 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 20:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.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 20:43:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:43:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:43:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:09: 1000000 INFO @ Sun, 21 Jun 2020 20:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.10_summits.bed INFO @ Sun, 21 Jun 2020 20:43:13: Done! pass1 - making usageList (117 chroms): 1 millis pass2 - checking and writing primary data (5905 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:43:20: 3000000 INFO @ Sun, 21 Jun 2020 20:43:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:43:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:43:24: #1 total tags in treatment: 3794588 INFO @ Sun, 21 Jun 2020 20:43:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:24: #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 20:43:25: #1 tags after filtering in treatment: 3794335 INFO @ Sun, 21 Jun 2020 20:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:25: #2 number of paired peaks: 7069 INFO @ Sun, 21 Jun 2020 20:43:25: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:25: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:25: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:25: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:25: #2 predicted fragment length is 307 bps INFO @ Sun, 21 Jun 2020 20:43:25: #2 alternative fragment length(s) may be 307 bps INFO @ Sun, 21 Jun 2020 20:43:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.20_model.r INFO @ Sun, 21 Jun 2020 20:43:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:43:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563529/SRX4563529.20_summits.bed INFO @ Sun, 21 Jun 2020 20:43:43: Done! pass1 - making usageList (72 chroms): 2 millis pass2 - checking and writing primary data (4524 records, 4 fields): 7 millis CompletedMACS2peakCalling