Job ID = 6456649 SRX = SRX3873747 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:04:54 prefetch.2.10.7: 1) Downloading 'SRR6927812'... 2020-06-21T11:04:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:05:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:05:47 prefetch.2.10.7: 'SRR6927812' is valid 2020-06-21T11:05:47 prefetch.2.10.7: 1) 'SRR6927812' was downloaded successfully 2020-06-21T11:05:47 prefetch.2.10.7: 'SRR6927812' has 0 unresolved dependencies Read 6636856 spots for SRR6927812/SRR6927812.sra Written 6636856 spots for SRR6927812/SRR6927812.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: 00:01:23 6636856 reads; of these: 6636856 (100.00%) were unpaired; of these: 838538 (12.63%) aligned 0 times 4818347 (72.60%) aligned exactly 1 time 979971 (14.77%) aligned >1 times 87.37% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 1149700 / 5798318 = 0.1983 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 20:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.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 20:09:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:09:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:09:57: 1000000 INFO @ Sun, 21 Jun 2020 20:10:02: 2000000 INFO @ Sun, 21 Jun 2020 20:10:08: 3000000 INFO @ Sun, 21 Jun 2020 20:10:14: 4000000 INFO @ Sun, 21 Jun 2020 20:10:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:10:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:10:18: #1 total tags in treatment: 4648618 INFO @ Sun, 21 Jun 2020 20:10:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:18: #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 20:10:18: #1 tags after filtering in treatment: 4648286 INFO @ Sun, 21 Jun 2020 20:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:18: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:10:19: #2 number of paired peaks: 3967 INFO @ Sun, 21 Jun 2020 20:10:19: start model_add_line... 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 20:10:19: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:19: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:19: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:19: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 20:10:19: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 21 Jun 2020 20:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.05_model.r INFO @ Sun, 21 Jun 2020 20:10:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.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 20:10:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:27: 1000000 INFO @ Sun, 21 Jun 2020 20:10:32: 2000000 INFO @ Sun, 21 Jun 2020 20:10:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:10:38: 3000000 INFO @ Sun, 21 Jun 2020 20:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.05_summits.bed INFO @ Sun, 21 Jun 2020 20:10:39: Done! pass1 - making usageList (140 chroms): 2 millis pass2 - checking and writing primary data (5301 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:10:44: 4000000 INFO @ Sun, 21 Jun 2020 20:10:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:10:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:10:48: #1 total tags in treatment: 4648618 INFO @ Sun, 21 Jun 2020 20:10:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:10:48: #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 20:10:49: #1 tags after filtering in treatment: 4648286 INFO @ Sun, 21 Jun 2020 20:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:10:49: #1 finished! INFO @ Sun, 21 Jun 2020 20:10:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:10:49: #2 looking for paired plus/minus strand peaks... 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 20:10:49: #2 number of paired peaks: 3967 INFO @ Sun, 21 Jun 2020 20:10:49: start model_add_line... INFO @ Sun, 21 Jun 2020 20:10:49: start X-correlation... INFO @ Sun, 21 Jun 2020 20:10:49: end of X-cor INFO @ Sun, 21 Jun 2020 20:10:49: #2 finished! INFO @ Sun, 21 Jun 2020 20:10:49: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 20:10:49: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 21 Jun 2020 20:10:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.10_model.r INFO @ Sun, 21 Jun 2020 20:10:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:10:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:10:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.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 20:10:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:10:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:10:57: 1000000 INFO @ Sun, 21 Jun 2020 20:11:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:03: 2000000 INFO @ Sun, 21 Jun 2020 20:11:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.10_summits.bed INFO @ Sun, 21 Jun 2020 20:11:08: Done! pass1 - making usageList (94 chroms): 1 millis pass2 - checking and writing primary data (3481 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:11:09: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:11:16: 4000000 INFO @ Sun, 21 Jun 2020 20:11:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:11:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:11:20: #1 total tags in treatment: 4648618 INFO @ Sun, 21 Jun 2020 20:11:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:11:20: #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 20:11:21: #1 tags after filtering in treatment: 4648286 INFO @ Sun, 21 Jun 2020 20:11:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:11:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:11:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:11:21: #2 number of paired peaks: 3967 INFO @ Sun, 21 Jun 2020 20:11:21: start model_add_line... INFO @ Sun, 21 Jun 2020 20:11:21: start X-correlation... INFO @ Sun, 21 Jun 2020 20:11:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:11:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:11:21: #2 predicted fragment length is 167 bps INFO @ Sun, 21 Jun 2020 20:11:21: #2 alternative fragment length(s) may be 167 bps INFO @ Sun, 21 Jun 2020 20:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.20_model.r INFO @ Sun, 21 Jun 2020 20:11:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:11:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:11:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3873747/SRX3873747.20_summits.bed INFO @ Sun, 21 Jun 2020 20:11:41: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (2126 records, 4 fields): 8 millis CompletedMACS2peakCalling