Job ID = 6368159 SRX = SRX494843 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:08:39 prefetch.2.10.7: 1) Downloading 'SRR1198375'... 2020-06-16T00:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:16 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:16 prefetch.2.10.7: 1) 'SRR1198375' was downloaded successfully Read 15611842 spots for SRR1198375/SRR1198375.sra Written 15611842 spots for SRR1198375/SRR1198375.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: 00:02:48 15611842 reads; of these: 15611842 (100.00%) were unpaired; of these: 956037 (6.12%) aligned 0 times 9800967 (62.78%) aligned exactly 1 time 4854838 (31.10%) aligned >1 times 93.88% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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_rmdupse_core] 6904915 / 14655805 = 0.4711 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 09:19:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.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 09:19:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:08: 1000000 INFO @ Tue, 16 Jun 2020 09:19:13: 2000000 INFO @ Tue, 16 Jun 2020 09:19:19: 3000000 INFO @ Tue, 16 Jun 2020 09:19:24: 4000000 INFO @ Tue, 16 Jun 2020 09:19:30: 5000000 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 09:19:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.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 09:19:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:36: 6000000 INFO @ Tue, 16 Jun 2020 09:19:39: 1000000 INFO @ Tue, 16 Jun 2020 09:19:43: 7000000 INFO @ Tue, 16 Jun 2020 09:19:47: 2000000 INFO @ Tue, 16 Jun 2020 09:19:48: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:48: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:48: #1 total tags in treatment: 7750890 INFO @ Tue, 16 Jun 2020 09:19:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:48: #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 09:19:48: #1 tags after filtering in treatment: 7750890 INFO @ Tue, 16 Jun 2020 09:19:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:49: #2 number of paired peaks: 5939 INFO @ Tue, 16 Jun 2020 09:19:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:49: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 09:19:49: #2 alternative fragment length(s) may be 3,202,216 bps INFO @ Tue, 16 Jun 2020 09:19:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.05_model.r INFO @ Tue, 16 Jun 2020 09:19:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:54: 3000000 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 09:20:00: 4000000 INFO @ Tue, 16 Jun 2020 09:20:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.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 09:20:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:08: 5000000 INFO @ Tue, 16 Jun 2020 09:20:09: 1000000 INFO @ Tue, 16 Jun 2020 09:20:15: 6000000 INFO @ Tue, 16 Jun 2020 09:20:17: 2000000 INFO @ Tue, 16 Jun 2020 09:20:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:22: 7000000 INFO @ Tue, 16 Jun 2020 09:20:24: 3000000 INFO @ Tue, 16 Jun 2020 09:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3497 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:28: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:28: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:28: #1 total tags in treatment: 7750890 INFO @ Tue, 16 Jun 2020 09:20:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:28: #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 09:20:28: #1 tags after filtering in treatment: 7750890 INFO @ Tue, 16 Jun 2020 09:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:29: #2 number of paired peaks: 5939 INFO @ Tue, 16 Jun 2020 09:20:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:29: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 09:20:29: #2 alternative fragment length(s) may be 3,202,216 bps INFO @ Tue, 16 Jun 2020 09:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.10_model.r INFO @ Tue, 16 Jun 2020 09:20:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:32: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:38: 5000000 INFO @ Tue, 16 Jun 2020 09:20:45: 6000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:52: 7000000 INFO @ Tue, 16 Jun 2020 09:20:57: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:57: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:57: #1 total tags in treatment: 7750890 INFO @ Tue, 16 Jun 2020 09:20:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:57: #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 09:20:57: #1 tags after filtering in treatment: 7750890 INFO @ Tue, 16 Jun 2020 09:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:58: #2 number of paired peaks: 5939 INFO @ Tue, 16 Jun 2020 09:20:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:58: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 09:20:58: #2 alternative fragment length(s) may be 3,202,216 bps INFO @ Tue, 16 Jun 2020 09:20:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.20_model.r INFO @ Tue, 16 Jun 2020 09:20:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:07: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1990 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494843/SRX494843.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (781 records, 4 fields): 2 millis CompletedMACS2peakCalling