Job ID = 6368364 SRX = SRX495044 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:47 prefetch.2.10.7: 1) Downloading 'SRR1198576'... 2020-06-16T00:14:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:20:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:20:23 prefetch.2.10.7: 1) 'SRR1198576' was downloaded successfully Read 27236726 spots for SRR1198576/SRR1198576.sra Written 27236726 spots for SRR1198576/SRR1198576.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: 00:00:01 Multiseed full-index search: 00:05:33 27236726 reads; of these: 27236726 (100.00%) were unpaired; of these: 3797086 (13.94%) aligned 0 times 20850927 (76.55%) aligned exactly 1 time 2588713 (9.50%) aligned >1 times 86.06% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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 12 files... [bam_rmdupse_core] 12247300 / 23439640 = 0.5225 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 09:32:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.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 09:32:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:31: 1000000 INFO @ Tue, 16 Jun 2020 09:32:36: 2000000 INFO @ Tue, 16 Jun 2020 09:32:42: 3000000 INFO @ Tue, 16 Jun 2020 09:32:47: 4000000 INFO @ Tue, 16 Jun 2020 09:32:53: 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 09:32:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.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 09:32:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:59: 6000000 INFO @ Tue, 16 Jun 2020 09:33:01: 1000000 INFO @ Tue, 16 Jun 2020 09:33:04: 7000000 INFO @ Tue, 16 Jun 2020 09:33:07: 2000000 INFO @ Tue, 16 Jun 2020 09:33:10: 8000000 INFO @ Tue, 16 Jun 2020 09:33:13: 3000000 INFO @ Tue, 16 Jun 2020 09:33:16: 9000000 INFO @ Tue, 16 Jun 2020 09:33:19: 4000000 INFO @ Tue, 16 Jun 2020 09:33:21: 10000000 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 09:33:24: 5000000 INFO @ Tue, 16 Jun 2020 09:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.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 09:33:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:27: 11000000 INFO @ Tue, 16 Jun 2020 09:33:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:33:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:33:28: #1 total tags in treatment: 11192340 INFO @ Tue, 16 Jun 2020 09:33:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:28: #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 09:33:29: #1 tags after filtering in treatment: 11192340 INFO @ Tue, 16 Jun 2020 09:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:29: #2 number of paired peaks: 990 WARNING @ Tue, 16 Jun 2020 09:33:29: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:30: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:33:30: #2 alternative fragment length(s) may be 3,110,131,150 bps INFO @ Tue, 16 Jun 2020 09:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.05_model.r INFO @ Tue, 16 Jun 2020 09:33:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:30: 6000000 INFO @ Tue, 16 Jun 2020 09:33:32: 1000000 INFO @ Tue, 16 Jun 2020 09:33:36: 7000000 INFO @ Tue, 16 Jun 2020 09:33:39: 2000000 INFO @ Tue, 16 Jun 2020 09:33:42: 8000000 INFO @ Tue, 16 Jun 2020 09:33:45: 3000000 INFO @ Tue, 16 Jun 2020 09:33:48: 9000000 INFO @ Tue, 16 Jun 2020 09:33:52: 4000000 INFO @ Tue, 16 Jun 2020 09:33:54: 10000000 INFO @ Tue, 16 Jun 2020 09:33:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:58: 5000000 INFO @ Tue, 16 Jun 2020 09:34:00: 11000000 INFO @ Tue, 16 Jun 2020 09:34:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:34:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:34:01: #1 total tags in treatment: 11192340 INFO @ Tue, 16 Jun 2020 09:34:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:01: #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 09:34:01: #1 tags after filtering in treatment: 11192340 INFO @ Tue, 16 Jun 2020 09:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:02: #2 number of paired peaks: 990 WARNING @ Tue, 16 Jun 2020 09:34:02: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:02: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:34:02: #2 alternative fragment length(s) may be 3,110,131,150 bps INFO @ Tue, 16 Jun 2020 09:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.10_model.r INFO @ Tue, 16 Jun 2020 09:34:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:05: 6000000 INFO @ Tue, 16 Jun 2020 09:34:11: 7000000 INFO @ Tue, 16 Jun 2020 09:34:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.05_summits.bed INFO @ Tue, 16 Jun 2020 09:34:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7629 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:17: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:34:23: 9000000 INFO @ Tue, 16 Jun 2020 09:34:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:30: 10000000 INFO @ Tue, 16 Jun 2020 09:34:36: 11000000 INFO @ Tue, 16 Jun 2020 09:34:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:34:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:34:37: #1 total tags in treatment: 11192340 INFO @ Tue, 16 Jun 2020 09:34:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:37: #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 09:34:37: #1 tags after filtering in treatment: 11192340 INFO @ Tue, 16 Jun 2020 09:34:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:38: #2 number of paired peaks: 990 WARNING @ Tue, 16 Jun 2020 09:34:38: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:38: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:34:38: #2 alternative fragment length(s) may be 3,110,131,150 bps INFO @ Tue, 16 Jun 2020 09:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.20_model.r INFO @ Tue, 16 Jun 2020 09:34:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.10_summits.bed INFO @ Tue, 16 Jun 2020 09:34:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2608 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:35:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495044/SRX495044.20_summits.bed INFO @ Tue, 16 Jun 2020 09:35:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling