Job ID = 6366735 SRX = SRX2228888 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:04:53 prefetch.2.10.7: 1) Downloading 'SRR4380344'... 2020-06-15T23:04:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:31 prefetch.2.10.7: 'SRR4380344' is valid 2020-06-15T23:05:31 prefetch.2.10.7: 1) 'SRR4380344' was downloaded successfully 2020-06-15T23:05:31 prefetch.2.10.7: 'SRR4380344' has 0 unresolved dependencies Read 10153262 spots for SRR4380344/SRR4380344.sra Written 10153262 spots for SRR4380344/SRR4380344.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: 00:02:04 10153262 reads; of these: 10153262 (100.00%) were unpaired; of these: 1777147 (17.50%) aligned 0 times 7066099 (69.59%) aligned exactly 1 time 1310016 (12.90%) aligned >1 times 82.50% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 1428671 / 8376115 = 0.1706 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 08:10:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.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 08:10:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:40: 1000000 INFO @ Tue, 16 Jun 2020 08:10:45: 2000000 INFO @ Tue, 16 Jun 2020 08:10:50: 3000000 INFO @ Tue, 16 Jun 2020 08:10:54: 4000000 INFO @ Tue, 16 Jun 2020 08:10:59: 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 08:11:04: 6000000 INFO @ Tue, 16 Jun 2020 08:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.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 08:11:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:08: #1 total tags in treatment: 6947444 INFO @ Tue, 16 Jun 2020 08:11:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:08: #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 08:11:09: #1 tags after filtering in treatment: 6947444 INFO @ Tue, 16 Jun 2020 08:11:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:09: #2 number of paired peaks: 893 WARNING @ Tue, 16 Jun 2020 08:11:09: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:09: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:11:09: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.05_model.r INFO @ Tue, 16 Jun 2020 08:11:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:10: 1000000 INFO @ Tue, 16 Jun 2020 08:11:15: 2000000 INFO @ Tue, 16 Jun 2020 08:11:20: 3000000 INFO @ Tue, 16 Jun 2020 08:11:24: 4000000 INFO @ Tue, 16 Jun 2020 08:11:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:29: 5000000 INFO @ Tue, 16 Jun 2020 08:11:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1754 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:11:34: 6000000 INFO @ Tue, 16 Jun 2020 08:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.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 08:11:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:38: #1 total tags in treatment: 6947444 INFO @ Tue, 16 Jun 2020 08:11:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:38: #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 08:11:38: #1 tags after filtering in treatment: 6947444 INFO @ Tue, 16 Jun 2020 08:11:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:39: #2 number of paired peaks: 893 WARNING @ Tue, 16 Jun 2020 08:11:39: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:39: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:11:39: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.10_model.r INFO @ Tue, 16 Jun 2020 08:11:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:40: 1000000 INFO @ Tue, 16 Jun 2020 08:11:45: 2000000 INFO @ Tue, 16 Jun 2020 08:11:50: 3000000 INFO @ Tue, 16 Jun 2020 08:11:55: 4000000 INFO @ Tue, 16 Jun 2020 08:11:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:00: 5000000 INFO @ Tue, 16 Jun 2020 08:12:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.10_summits.bed INFO @ Tue, 16 Jun 2020 08:12:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1140 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:12:05: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:12:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:09: #1 total tags in treatment: 6947444 INFO @ Tue, 16 Jun 2020 08:12:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:09: #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 08:12:09: #1 tags after filtering in treatment: 6947444 INFO @ Tue, 16 Jun 2020 08:12:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:09: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:10: #2 number of paired peaks: 893 WARNING @ Tue, 16 Jun 2020 08:12:10: Fewer paired peaks (893) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 893 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:10: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:10: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:10: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 08:12:10: #2 alternative fragment length(s) may be 142 bps INFO @ Tue, 16 Jun 2020 08:12:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.20_model.r INFO @ Tue, 16 Jun 2020 08:12:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:12:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228888/SRX2228888.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (713 records, 4 fields): 2 millis CompletedMACS2peakCalling