Job ID = 6366701 SRX = SRX2228857 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:08 prefetch.2.10.7: 1) Downloading 'SRR4380313'... 2020-06-15T22:59:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:52 prefetch.2.10.7: 'SRR4380313' is valid 2020-06-15T22:59:52 prefetch.2.10.7: 1) 'SRR4380313' was downloaded successfully Read 11801157 spots for SRR4380313/SRR4380313.sra Written 11801157 spots for SRR4380313/SRR4380313.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: 00:02:16 11801157 reads; of these: 11801157 (100.00%) were unpaired; of these: 1018050 (8.63%) aligned 0 times 8926039 (75.64%) aligned exactly 1 time 1857068 (15.74%) aligned >1 times 91.37% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 5966163 / 10783107 = 0.5533 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 08:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.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 08:05:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:15: 1000000 INFO @ Tue, 16 Jun 2020 08:05:20: 2000000 INFO @ Tue, 16 Jun 2020 08:05:25: 3000000 INFO @ Tue, 16 Jun 2020 08:05:31: 4000000 INFO @ Tue, 16 Jun 2020 08:05:35: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:05:35: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:05:35: #1 total tags in treatment: 4816944 INFO @ Tue, 16 Jun 2020 08:05:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:35: #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 08:05:35: #1 tags after filtering in treatment: 4816944 INFO @ Tue, 16 Jun 2020 08:05:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:36: #2 number of paired peaks: 720 WARNING @ Tue, 16 Jun 2020 08:05:36: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:36: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:05:36: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 08:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.05_model.r INFO @ Tue, 16 Jun 2020 08:05:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:36: #3 Pre-compute pvalue-qvalue table... 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 08:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.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 08:05:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:44: 1000000 INFO @ Tue, 16 Jun 2020 08:05:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:49: 2000000 INFO @ Tue, 16 Jun 2020 08:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.05_summits.bed INFO @ Tue, 16 Jun 2020 08:05:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1091 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:54: 3000000 INFO @ Tue, 16 Jun 2020 08:05:59: 4000000 INFO @ Tue, 16 Jun 2020 08:06:03: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:06:03: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:06:03: #1 total tags in treatment: 4816944 INFO @ Tue, 16 Jun 2020 08:06:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:03: #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 08:06:03: #1 tags after filtering in treatment: 4816944 INFO @ Tue, 16 Jun 2020 08:06:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:03: #2 number of paired peaks: 720 WARNING @ Tue, 16 Jun 2020 08:06:03: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:03: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:06:03: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 08:06:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.10_model.r INFO @ Tue, 16 Jun 2020 08:06:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:03: #3 Pre-compute pvalue-qvalue table... 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 08:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.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 08:06:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:15: 1000000 INFO @ Tue, 16 Jun 2020 08:06:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (543 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:20: 2000000 INFO @ Tue, 16 Jun 2020 08:06:26: 3000000 INFO @ Tue, 16 Jun 2020 08:06:31: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:36: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:06:36: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:06:36: #1 total tags in treatment: 4816944 INFO @ Tue, 16 Jun 2020 08:06:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:36: #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 08:06:36: #1 tags after filtering in treatment: 4816944 INFO @ Tue, 16 Jun 2020 08:06:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:36: #2 number of paired peaks: 720 WARNING @ Tue, 16 Jun 2020 08:06:36: Fewer paired peaks (720) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 720 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:36: #2 predicted fragment length is 129 bps INFO @ Tue, 16 Jun 2020 08:06:36: #2 alternative fragment length(s) may be 4,129 bps INFO @ Tue, 16 Jun 2020 08:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.20_model.r INFO @ Tue, 16 Jun 2020 08:06:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:06:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228857/SRX2228857.20_summits.bed INFO @ Tue, 16 Jun 2020 08:06:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 millis CompletedMACS2peakCalling