Job ID = 6366931 SRX = SRX2576633 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:53 prefetch.2.10.7: 1) Downloading 'SRR5272590'... 2020-06-15T23:05:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:59 prefetch.2.10.7: 'SRR5272590' is valid 2020-06-15T23:06:59 prefetch.2.10.7: 1) 'SRR5272590' was downloaded successfully Read 17967710 spots for SRR5272590/SRR5272590.sra Written 17967710 spots for SRR5272590/SRR5272590.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: 00:02:46 17967710 reads; of these: 17967710 (100.00%) were unpaired; of these: 1836464 (10.22%) aligned 0 times 13420557 (74.69%) aligned exactly 1 time 2710689 (15.09%) aligned >1 times 89.78% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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_rmdupse_core] 3453672 / 16131246 = 0.2141 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 08:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.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 08:14:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:30: 1000000 INFO @ Tue, 16 Jun 2020 08:14:35: 2000000 INFO @ Tue, 16 Jun 2020 08:14:40: 3000000 INFO @ Tue, 16 Jun 2020 08:14:46: 4000000 INFO @ Tue, 16 Jun 2020 08:14:51: 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 08:14:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.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 08:14:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:56: 6000000 INFO @ Tue, 16 Jun 2020 08:15:00: 1000000 INFO @ Tue, 16 Jun 2020 08:15:01: 7000000 INFO @ Tue, 16 Jun 2020 08:15:05: 2000000 INFO @ Tue, 16 Jun 2020 08:15:07: 8000000 INFO @ Tue, 16 Jun 2020 08:15:11: 3000000 INFO @ Tue, 16 Jun 2020 08:15:12: 9000000 INFO @ Tue, 16 Jun 2020 08:15:16: 4000000 INFO @ Tue, 16 Jun 2020 08:15:17: 10000000 INFO @ Tue, 16 Jun 2020 08:15:22: 5000000 INFO @ Tue, 16 Jun 2020 08:15:23: 11000000 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 08:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.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 08:15:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:27: 6000000 INFO @ Tue, 16 Jun 2020 08:15:29: 12000000 INFO @ Tue, 16 Jun 2020 08:15:31: 1000000 INFO @ Tue, 16 Jun 2020 08:15:33: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:15:33: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:15:33: #1 total tags in treatment: 12677574 INFO @ Tue, 16 Jun 2020 08:15:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:33: #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 08:15:33: #1 tags after filtering in treatment: 12677574 INFO @ Tue, 16 Jun 2020 08:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:33: 7000000 INFO @ Tue, 16 Jun 2020 08:15:34: #2 number of paired peaks: 602 WARNING @ Tue, 16 Jun 2020 08:15:34: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:34: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:15:34: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 16 Jun 2020 08:15:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.05_model.r INFO @ Tue, 16 Jun 2020 08:15:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:37: 2000000 INFO @ Tue, 16 Jun 2020 08:15:39: 8000000 INFO @ Tue, 16 Jun 2020 08:15:43: 3000000 INFO @ Tue, 16 Jun 2020 08:15:45: 9000000 INFO @ Tue, 16 Jun 2020 08:15:49: 4000000 INFO @ Tue, 16 Jun 2020 08:15:51: 10000000 INFO @ Tue, 16 Jun 2020 08:15:55: 5000000 INFO @ Tue, 16 Jun 2020 08:15:57: 11000000 INFO @ Tue, 16 Jun 2020 08:16:01: 6000000 INFO @ Tue, 16 Jun 2020 08:16:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:04: 12000000 INFO @ Tue, 16 Jun 2020 08:16:07: 7000000 INFO @ Tue, 16 Jun 2020 08:16:08: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:16:08: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:16:08: #1 total tags in treatment: 12677574 INFO @ Tue, 16 Jun 2020 08:16:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:08: #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 08:16:08: #1 tags after filtering in treatment: 12677574 INFO @ Tue, 16 Jun 2020 08:16:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:09: #2 number of paired peaks: 602 WARNING @ Tue, 16 Jun 2020 08:16:09: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:09: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:16:09: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 16 Jun 2020 08:16:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.10_model.r INFO @ Tue, 16 Jun 2020 08:16:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:13: 8000000 INFO @ Tue, 16 Jun 2020 08:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.05_summits.bed INFO @ Tue, 16 Jun 2020 08:16:16: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6768 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:18: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:24: 10000000 INFO @ Tue, 16 Jun 2020 08:16:29: 11000000 INFO @ Tue, 16 Jun 2020 08:16:35: 12000000 INFO @ Tue, 16 Jun 2020 08:16:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 08:16:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 08:16:39: #1 total tags in treatment: 12677574 INFO @ Tue, 16 Jun 2020 08:16:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:39: #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 08:16:39: #1 tags after filtering in treatment: 12677574 INFO @ Tue, 16 Jun 2020 08:16:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:40: #2 number of paired peaks: 602 WARNING @ Tue, 16 Jun 2020 08:16:40: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:40: #2 predicted fragment length is 119 bps INFO @ Tue, 16 Jun 2020 08:16:40: #2 alternative fragment length(s) may be 119 bps INFO @ Tue, 16 Jun 2020 08:16:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.20_model.r INFO @ Tue, 16 Jun 2020 08:16:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3352 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:17:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576633/SRX2576633.20_summits.bed INFO @ Tue, 16 Jun 2020 08:17:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2056 records, 4 fields): 3 millis CompletedMACS2peakCalling