Job ID = 6368214 SRX = SRX494897 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:08:24 prefetch.2.10.7: 1) Downloading 'SRR1198429'... 2020-06-16T00:08:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:11:15 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:11:15 prefetch.2.10.7: 1) 'SRR1198429' was downloaded successfully Read 19681495 spots for SRR1198429/SRR1198429.sra Written 19681495 spots for SRR1198429/SRR1198429.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: 00:03:53 19681495 reads; of these: 19681495 (100.00%) were unpaired; of these: 6163709 (31.32%) aligned 0 times 11157411 (56.69%) aligned exactly 1 time 2360375 (11.99%) aligned >1 times 68.68% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 7299558 / 13517786 = 0.5400 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 09:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.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 09:19:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:38: 1000000 INFO @ Tue, 16 Jun 2020 09:19:46: 2000000 INFO @ Tue, 16 Jun 2020 09:19:54: 3000000 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 09:20:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.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 09:20:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:02: 4000000 INFO @ Tue, 16 Jun 2020 09:20:09: 1000000 INFO @ Tue, 16 Jun 2020 09:20:10: 5000000 INFO @ Tue, 16 Jun 2020 09:20:17: 2000000 INFO @ Tue, 16 Jun 2020 09:20:19: 6000000 INFO @ Tue, 16 Jun 2020 09:20:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:21: #1 total tags in treatment: 6218228 INFO @ Tue, 16 Jun 2020 09:20:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:21: #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 09:20:21: #1 tags after filtering in treatment: 6218228 INFO @ Tue, 16 Jun 2020 09:20:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:21: #2 number of paired peaks: 592 WARNING @ Tue, 16 Jun 2020 09:20:21: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:21: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:20:21: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 09:20:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:21: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:21: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 09:20:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:20:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:26: 3000000 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 09:20:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.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 09:20:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:34: 4000000 INFO @ Tue, 16 Jun 2020 09:20:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:39: 1000000 INFO @ Tue, 16 Jun 2020 09:20:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (795 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:43: 5000000 INFO @ Tue, 16 Jun 2020 09:20:48: 2000000 INFO @ Tue, 16 Jun 2020 09:20:51: 6000000 INFO @ Tue, 16 Jun 2020 09:20:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:20:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:20:53: #1 total tags in treatment: 6218228 INFO @ Tue, 16 Jun 2020 09:20:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:53: #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 09:20:53: #1 tags after filtering in treatment: 6218228 INFO @ Tue, 16 Jun 2020 09:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:54: #2 number of paired peaks: 592 WARNING @ Tue, 16 Jun 2020 09:20:54: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:54: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:20:54: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 09:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:54: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 09:20:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:20:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:57: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:05: 4000000 INFO @ Tue, 16 Jun 2020 09:21:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:12: 5000000 INFO @ Tue, 16 Jun 2020 09:21:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (574 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:20: 6000000 INFO @ Tue, 16 Jun 2020 09:21:22: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:22: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:22: #1 total tags in treatment: 6218228 INFO @ Tue, 16 Jun 2020 09:21:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:22: #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 09:21:22: #1 tags after filtering in treatment: 6218228 INFO @ Tue, 16 Jun 2020 09:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:22: #2 number of paired peaks: 592 WARNING @ Tue, 16 Jun 2020 09:21:22: Fewer paired peaks (592) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 592 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:22: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:21:22: #2 alternative fragment length(s) may be 4,48 bps INFO @ Tue, 16 Jun 2020 09:21:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:22: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Tue, 16 Jun 2020 09:21:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:21:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494897/SRX494897.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling