Job ID = 6457558 SRX = SRX4669047 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:44:03 prefetch.2.10.7: 1) Downloading 'SRR7817572'... 2020-06-21T11:44:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:46:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:46:48 prefetch.2.10.7: 'SRR7817572' is valid 2020-06-21T11:46:48 prefetch.2.10.7: 1) 'SRR7817572' was downloaded successfully 2020-06-21T11:46:48 prefetch.2.10.7: 'SRR7817572' has 0 unresolved dependencies Read 26568670 spots for SRR7817572/SRR7817572.sra Written 26568670 spots for SRR7817572/SRR7817572.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:55 26568670 reads; of these: 26568670 (100.00%) were unpaired; of these: 3880547 (14.61%) aligned 0 times 17900005 (67.37%) aligned exactly 1 time 4788118 (18.02%) aligned >1 times 85.39% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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 12 files... [bam_rmdupse_core] 9436028 / 22688123 = 0.4159 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 20:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.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 20:57:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:58:04: 1000000 INFO @ Sun, 21 Jun 2020 20:58:10: 2000000 INFO @ Sun, 21 Jun 2020 20:58:16: 3000000 INFO @ Sun, 21 Jun 2020 20:58:22: 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 20:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.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 20:58:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:58:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:58:28: 5000000 INFO @ Sun, 21 Jun 2020 20:58:34: 1000000 INFO @ Sun, 21 Jun 2020 20:58:35: 6000000 INFO @ Sun, 21 Jun 2020 20:58:41: 2000000 INFO @ Sun, 21 Jun 2020 20:58:42: 7000000 INFO @ Sun, 21 Jun 2020 20:58:47: 3000000 INFO @ Sun, 21 Jun 2020 20:58:48: 8000000 INFO @ Sun, 21 Jun 2020 20:58:54: 4000000 INFO @ Sun, 21 Jun 2020 20:58:55: 9000000 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 20:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.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 20:58:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:58:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:59:01: 5000000 INFO @ Sun, 21 Jun 2020 20:59:02: 10000000 INFO @ Sun, 21 Jun 2020 20:59:04: 1000000 INFO @ Sun, 21 Jun 2020 20:59:07: 6000000 INFO @ Sun, 21 Jun 2020 20:59:09: 11000000 INFO @ Sun, 21 Jun 2020 20:59:10: 2000000 INFO @ Sun, 21 Jun 2020 20:59:14: 7000000 INFO @ Sun, 21 Jun 2020 20:59:16: 12000000 INFO @ Sun, 21 Jun 2020 20:59:16: 3000000 INFO @ Sun, 21 Jun 2020 20:59:21: 8000000 INFO @ Sun, 21 Jun 2020 20:59:22: 4000000 INFO @ Sun, 21 Jun 2020 20:59:23: 13000000 INFO @ Sun, 21 Jun 2020 20:59:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:59:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:59:25: #1 total tags in treatment: 13252095 INFO @ Sun, 21 Jun 2020 20:59:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:59:25: #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 20:59:25: #1 tags after filtering in treatment: 13252089 INFO @ Sun, 21 Jun 2020 20:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:59:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:59:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:59:26: #2 number of paired peaks: 2314 INFO @ Sun, 21 Jun 2020 20:59:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:59:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:59:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:59:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:59:26: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 20:59:26: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 20:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.05_model.r INFO @ Sun, 21 Jun 2020 20:59:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:59:28: 9000000 INFO @ Sun, 21 Jun 2020 20:59:28: 5000000 INFO @ Sun, 21 Jun 2020 20:59:34: 6000000 INFO @ Sun, 21 Jun 2020 20:59:35: 10000000 INFO @ Sun, 21 Jun 2020 20:59:40: 7000000 INFO @ Sun, 21 Jun 2020 20:59:42: 11000000 INFO @ Sun, 21 Jun 2020 20:59:46: 8000000 INFO @ Sun, 21 Jun 2020 20:59:49: 12000000 INFO @ Sun, 21 Jun 2020 20:59:52: 9000000 INFO @ Sun, 21 Jun 2020 20:59:56: 13000000 INFO @ Sun, 21 Jun 2020 20:59:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:59:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:59:58: #1 total tags in treatment: 13252095 INFO @ Sun, 21 Jun 2020 20:59:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:59:58: #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 20:59:58: #1 tags after filtering in treatment: 13252089 INFO @ Sun, 21 Jun 2020 20:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:59:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:59:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:59:58: 10000000 INFO @ Sun, 21 Jun 2020 20:59:59: #2 number of paired peaks: 2314 INFO @ Sun, 21 Jun 2020 20:59:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:59:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:59:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:59:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:59:59: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 20:59:59: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 20:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.10_model.r INFO @ Sun, 21 Jun 2020 20:59:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:59:59: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:00:04: 11000000 INFO @ Sun, 21 Jun 2020 21:00:09: 12000000 INFO @ Sun, 21 Jun 2020 21:00:15: 13000000 INFO @ Sun, 21 Jun 2020 21:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:00:16: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:00:16: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:00:16: #1 total tags in treatment: 13252095 INFO @ Sun, 21 Jun 2020 21:00:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:00:16: #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 21:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.05_summits.bed INFO @ Sun, 21 Jun 2020 21:00:16: Done! INFO @ Sun, 21 Jun 2020 21:00:17: #1 tags after filtering in treatment: 13252089 INFO @ Sun, 21 Jun 2020 21:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:00:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:00:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:00:17: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (571 chroms): 3 millis pass2 - checking and writing primary data (10693 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:00:18: #2 number of paired peaks: 2314 INFO @ Sun, 21 Jun 2020 21:00:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:00:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:00:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:00:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:00:18: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 21:00:18: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 21:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.20_model.r INFO @ Sun, 21 Jun 2020 21:00:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:00:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:00:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:00:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:00:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:00:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.10_summits.bed INFO @ Sun, 21 Jun 2020 21:00:47: Done! pass1 - making usageList (354 chroms): 1 millis pass2 - checking and writing primary data (6965 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:00:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:01:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:01:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669047/SRX4669047.20_summits.bed INFO @ Sun, 21 Jun 2020 21:01:06: Done! pass1 - making usageList (152 chroms): 1 millis pass2 - checking and writing primary data (3618 records, 4 fields): 8 millis CompletedMACS2peakCalling