Job ID = 6367146 SRX = SRX277104 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:18 prefetch.2.10.7: 1) Downloading 'SRR849780'... 2020-06-15T23:14:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:14:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:14:58 prefetch.2.10.7: 'SRR849780' is valid 2020-06-15T23:14:58 prefetch.2.10.7: 1) 'SRR849780' was downloaded successfully Read 7590261 spots for SRR849780/SRR849780.sra Written 7590261 spots for SRR849780/SRR849780.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: 00:00:58 7590261 reads; of these: 7590261 (100.00%) were unpaired; of these: 2768485 (36.47%) aligned 0 times 4163905 (54.86%) aligned exactly 1 time 657871 (8.67%) aligned >1 times 63.53% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 697922 / 4821776 = 0.1447 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 08:17:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.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 08:17:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:47: 1000000 INFO @ Tue, 16 Jun 2020 08:17:53: 2000000 INFO @ Tue, 16 Jun 2020 08:17:59: 3000000 INFO @ Tue, 16 Jun 2020 08:18:05: 4000000 INFO @ Tue, 16 Jun 2020 08:18:06: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:18:06: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:18:06: #1 total tags in treatment: 4123854 INFO @ Tue, 16 Jun 2020 08:18:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:06: #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 08:18:06: #1 tags after filtering in treatment: 4123854 INFO @ Tue, 16 Jun 2020 08:18:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:06: #2 number of paired peaks: 937 WARNING @ Tue, 16 Jun 2020 08:18:06: Fewer paired peaks (937) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 937 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:06: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:18:06: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.05_model.r INFO @ Tue, 16 Jun 2020 08:18:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:06: #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 08:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.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 08:18:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:17: 1000000 INFO @ Tue, 16 Jun 2020 08:18:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2896 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:22: 2000000 INFO @ Tue, 16 Jun 2020 08:18:27: 3000000 INFO @ Tue, 16 Jun 2020 08:18:32: 4000000 INFO @ Tue, 16 Jun 2020 08:18:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:18:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:18:32: #1 total tags in treatment: 4123854 INFO @ Tue, 16 Jun 2020 08:18:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:32: #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 08:18:33: #1 tags after filtering in treatment: 4123854 INFO @ Tue, 16 Jun 2020 08:18:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:33: #2 number of paired peaks: 937 WARNING @ Tue, 16 Jun 2020 08:18:33: Fewer paired peaks (937) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 937 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:33: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:18:33: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:18:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.10_model.r INFO @ Tue, 16 Jun 2020 08:18:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:33: #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 08:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.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 08:18:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:46: 1000000 INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1483 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:51: 2000000 INFO @ Tue, 16 Jun 2020 08:18:56: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:01: 4000000 INFO @ Tue, 16 Jun 2020 08:19:02: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:19:02: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:19:02: #1 total tags in treatment: 4123854 INFO @ Tue, 16 Jun 2020 08:19:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:02: #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 08:19:02: #1 tags after filtering in treatment: 4123854 INFO @ Tue, 16 Jun 2020 08:19:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:02: #2 number of paired peaks: 937 WARNING @ Tue, 16 Jun 2020 08:19:02: Fewer paired peaks (937) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 937 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:02: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 08:19:02: #2 alternative fragment length(s) may be 149 bps INFO @ Tue, 16 Jun 2020 08:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.20_model.r INFO @ Tue, 16 Jun 2020 08:19:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277104/SRX277104.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (614 records, 4 fields): 2 millis CompletedMACS2peakCalling