Job ID = 6366590 SRX = SRX2035137 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:58:23 prefetch.2.10.7: 1) Downloading 'SRR4044261'... 2020-06-15T22:58:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:27 prefetch.2.10.7: 1) 'SRR4044261' was downloaded successfully Read 6426854 spots for SRR4044261/SRR4044261.sra Written 6426854 spots for SRR4044261/SRR4044261.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: 00:08:19 6426854 reads; of these: 6426854 (100.00%) were paired; of these: 1717891 (26.73%) aligned concordantly 0 times 4125103 (64.19%) aligned concordantly exactly 1 time 583860 (9.08%) aligned concordantly >1 times ---- 1717891 pairs aligned concordantly 0 times; of these: 331310 (19.29%) aligned discordantly 1 time ---- 1386581 pairs aligned 0 times concordantly or discordantly; of these: 2773162 mates make up the pairs; of these: 2631105 (94.88%) aligned 0 times 61429 (2.22%) aligned exactly 1 time 80628 (2.91%) aligned >1 times 79.53% overall alignment rate Time searching: 00:08:19 Overall time: 00:08:19 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 331627 / 5035105 = 0.0659 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 @ Tue, 16 Jun 2020 08:15:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:15:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:11: 1000000 INFO @ Tue, 16 Jun 2020 08:15:19: 2000000 INFO @ Tue, 16 Jun 2020 08:15:26: 3000000 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 @ Tue, 16 Jun 2020 08:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:15:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:35: 4000000 INFO @ Tue, 16 Jun 2020 08:15:41: 1000000 INFO @ Tue, 16 Jun 2020 08:15:44: 5000000 INFO @ Tue, 16 Jun 2020 08:15:51: 2000000 INFO @ Tue, 16 Jun 2020 08:15:53: 6000000 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 @ Tue, 16 Jun 2020 08:16:00: 3000000 INFO @ Tue, 16 Jun 2020 08:16:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:16:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:02: 7000000 INFO @ Tue, 16 Jun 2020 08:16:10: 4000000 INFO @ Tue, 16 Jun 2020 08:16:11: 1000000 INFO @ Tue, 16 Jun 2020 08:16:11: 8000000 INFO @ Tue, 16 Jun 2020 08:16:19: 5000000 INFO @ Tue, 16 Jun 2020 08:16:19: 2000000 INFO @ Tue, 16 Jun 2020 08:16:20: 9000000 INFO @ Tue, 16 Jun 2020 08:16:25: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:16:25: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:16:25: #1 total tags in treatment: 4383682 INFO @ Tue, 16 Jun 2020 08:16:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:16:25: #1 tags after filtering in treatment: 4064516 INFO @ Tue, 16 Jun 2020 08:16:25: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:16:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:26: #2 number of paired peaks: 3297 INFO @ Tue, 16 Jun 2020 08:16:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:26: #2 predicted fragment length is 267 bps INFO @ Tue, 16 Jun 2020 08:16:26: #2 alternative fragment length(s) may be 267 bps INFO @ Tue, 16 Jun 2020 08:16:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.05_model.r INFO @ Tue, 16 Jun 2020 08:16:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:28: 3000000 INFO @ Tue, 16 Jun 2020 08:16:28: 6000000 INFO @ Tue, 16 Jun 2020 08:16:37: 4000000 INFO @ Tue, 16 Jun 2020 08:16:38: 7000000 INFO @ Tue, 16 Jun 2020 08:16:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.05_summits.bed INFO @ Tue, 16 Jun 2020 08:16:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3158 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:45: 5000000 INFO @ Tue, 16 Jun 2020 08:16:47: 8000000 INFO @ Tue, 16 Jun 2020 08:16:54: 6000000 INFO @ Tue, 16 Jun 2020 08:16:56: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:01: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:17:01: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:17:01: #1 total tags in treatment: 4383682 INFO @ Tue, 16 Jun 2020 08:17:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:17:02: #1 tags after filtering in treatment: 4064516 INFO @ Tue, 16 Jun 2020 08:17:02: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:17:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:02: #2 number of paired peaks: 3297 INFO @ Tue, 16 Jun 2020 08:17:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:02: #2 predicted fragment length is 267 bps INFO @ Tue, 16 Jun 2020 08:17:02: #2 alternative fragment length(s) may be 267 bps INFO @ Tue, 16 Jun 2020 08:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.10_model.r INFO @ Tue, 16 Jun 2020 08:17:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:03: 7000000 INFO @ Tue, 16 Jun 2020 08:17:10: 8000000 INFO @ Tue, 16 Jun 2020 08:17:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:17: 9000000 INFO @ Tue, 16 Jun 2020 08:17:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.10_summits.bed INFO @ Tue, 16 Jun 2020 08:17:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2545 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:17:21: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:17:21: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:17:21: #1 total tags in treatment: 4383682 INFO @ Tue, 16 Jun 2020 08:17:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:17:21: #1 tags after filtering in treatment: 4064516 INFO @ Tue, 16 Jun 2020 08:17:21: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 08:17:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:22: #2 number of paired peaks: 3297 INFO @ Tue, 16 Jun 2020 08:17:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:22: #2 predicted fragment length is 267 bps INFO @ Tue, 16 Jun 2020 08:17:22: #2 alternative fragment length(s) may be 267 bps INFO @ Tue, 16 Jun 2020 08:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.20_model.r INFO @ Tue, 16 Jun 2020 08:17:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2035137/SRX2035137.20_summits.bed INFO @ Tue, 16 Jun 2020 08:17:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2005 records, 4 fields): 4 millis CompletedMACS2peakCalling