Job ID = 6507840 SRX = SRX494839 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:49:28 prefetch.2.10.7: 1) Downloading 'SRR1198371'... 2020-06-26T13:49:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:51:42 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:51:42 prefetch.2.10.7: 1) 'SRR1198371' was downloaded successfully Read 21381473 spots for SRR1198371/SRR1198371.sra Written 21381473 spots for SRR1198371/SRR1198371.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: 00:04:55 21381473 reads; of these: 21381473 (100.00%) were unpaired; of these: 3814085 (17.84%) aligned 0 times 14578213 (68.18%) aligned exactly 1 time 2989175 (13.98%) aligned >1 times 82.16% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 4809603 / 17567388 = 0.2738 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 @ Fri, 26 Jun 2020 23:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.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 @ Fri, 26 Jun 2020 23:02:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:02:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:02:31: 1000000 INFO @ Fri, 26 Jun 2020 23:02:37: 2000000 INFO @ Fri, 26 Jun 2020 23:02:44: 3000000 INFO @ Fri, 26 Jun 2020 23:02:50: 4000000 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 @ Fri, 26 Jun 2020 23:02:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.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 @ Fri, 26 Jun 2020 23:02:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:02:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:02:57: 5000000 INFO @ Fri, 26 Jun 2020 23:03:01: 1000000 INFO @ Fri, 26 Jun 2020 23:03:04: 6000000 INFO @ Fri, 26 Jun 2020 23:03:09: 2000000 INFO @ Fri, 26 Jun 2020 23:03:11: 7000000 INFO @ Fri, 26 Jun 2020 23:03:16: 3000000 INFO @ Fri, 26 Jun 2020 23:03:19: 8000000 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 @ Fri, 26 Jun 2020 23:03:23: 4000000 INFO @ Fri, 26 Jun 2020 23:03:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.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 @ Fri, 26 Jun 2020 23:03:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:03:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:03:26: 9000000 INFO @ Fri, 26 Jun 2020 23:03:30: 5000000 INFO @ Fri, 26 Jun 2020 23:03:31: 1000000 INFO @ Fri, 26 Jun 2020 23:03:33: 10000000 INFO @ Fri, 26 Jun 2020 23:03:38: 6000000 INFO @ Fri, 26 Jun 2020 23:03:39: 2000000 INFO @ Fri, 26 Jun 2020 23:03:40: 11000000 INFO @ Fri, 26 Jun 2020 23:03:45: 7000000 INFO @ Fri, 26 Jun 2020 23:03:47: 3000000 INFO @ Fri, 26 Jun 2020 23:03:47: 12000000 INFO @ Fri, 26 Jun 2020 23:03:52: 8000000 INFO @ Fri, 26 Jun 2020 23:03:53: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:03:53: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:03:53: #1 total tags in treatment: 12757785 INFO @ Fri, 26 Jun 2020 23:03:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:03:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:03:53: #1 tags after filtering in treatment: 12757785 INFO @ Fri, 26 Jun 2020 23:03:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:03:53: #1 finished! INFO @ Fri, 26 Jun 2020 23:03:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:03:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:03:54: #2 number of paired peaks: 338 WARNING @ Fri, 26 Jun 2020 23:03:54: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Fri, 26 Jun 2020 23:03:54: start model_add_line... INFO @ Fri, 26 Jun 2020 23:03:54: start X-correlation... INFO @ Fri, 26 Jun 2020 23:03:54: end of X-cor INFO @ Fri, 26 Jun 2020 23:03:54: #2 finished! INFO @ Fri, 26 Jun 2020 23:03:54: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 23:03:54: #2 alternative fragment length(s) may be 2,46,562,567 bps INFO @ Fri, 26 Jun 2020 23:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.05_model.r WARNING @ Fri, 26 Jun 2020 23:03:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:03:54: #2 You may need to consider one of the other alternative d(s): 2,46,562,567 WARNING @ Fri, 26 Jun 2020 23:03:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:03:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:03:54: 4000000 INFO @ Fri, 26 Jun 2020 23:03:59: 9000000 INFO @ Fri, 26 Jun 2020 23:04:01: 5000000 INFO @ Fri, 26 Jun 2020 23:04:07: 10000000 INFO @ Fri, 26 Jun 2020 23:04:09: 6000000 INFO @ Fri, 26 Jun 2020 23:04:14: 11000000 INFO @ Fri, 26 Jun 2020 23:04:16: 7000000 INFO @ Fri, 26 Jun 2020 23:04:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:04:20: 12000000 INFO @ Fri, 26 Jun 2020 23:04:23: 8000000 INFO @ Fri, 26 Jun 2020 23:04:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:04:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:04:26: #1 total tags in treatment: 12757785 INFO @ Fri, 26 Jun 2020 23:04:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:04:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:04:26: #1 tags after filtering in treatment: 12757785 INFO @ Fri, 26 Jun 2020 23:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:04:26: #1 finished! INFO @ Fri, 26 Jun 2020 23:04:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:04:27: #2 number of paired peaks: 338 WARNING @ Fri, 26 Jun 2020 23:04:27: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Fri, 26 Jun 2020 23:04:27: start model_add_line... INFO @ Fri, 26 Jun 2020 23:04:27: start X-correlation... INFO @ Fri, 26 Jun 2020 23:04:27: end of X-cor INFO @ Fri, 26 Jun 2020 23:04:27: #2 finished! INFO @ Fri, 26 Jun 2020 23:04:27: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 23:04:27: #2 alternative fragment length(s) may be 2,46,562,567 bps INFO @ Fri, 26 Jun 2020 23:04:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.10_model.r WARNING @ Fri, 26 Jun 2020 23:04:27: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:04:27: #2 You may need to consider one of the other alternative d(s): 2,46,562,567 WARNING @ Fri, 26 Jun 2020 23:04:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:04:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:04:30: 9000000 INFO @ Fri, 26 Jun 2020 23:04:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:04:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:04:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.05_summits.bed INFO @ Fri, 26 Jun 2020 23:04:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (755 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:04:36: 10000000 INFO @ Fri, 26 Jun 2020 23:04:42: 11000000 INFO @ Fri, 26 Jun 2020 23:04:48: 12000000 INFO @ Fri, 26 Jun 2020 23:04:53: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:04:53: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:04:53: #1 total tags in treatment: 12757785 INFO @ Fri, 26 Jun 2020 23:04:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:04:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:04:53: #1 tags after filtering in treatment: 12757785 INFO @ Fri, 26 Jun 2020 23:04:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:04:53: #1 finished! INFO @ Fri, 26 Jun 2020 23:04:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:04:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:04:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:04:54: #2 number of paired peaks: 338 WARNING @ Fri, 26 Jun 2020 23:04:54: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Fri, 26 Jun 2020 23:04:54: start model_add_line... INFO @ Fri, 26 Jun 2020 23:04:54: start X-correlation... INFO @ Fri, 26 Jun 2020 23:04:54: end of X-cor INFO @ Fri, 26 Jun 2020 23:04:54: #2 finished! INFO @ Fri, 26 Jun 2020 23:04:54: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 23:04:54: #2 alternative fragment length(s) may be 2,46,562,567 bps INFO @ Fri, 26 Jun 2020 23:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.20_model.r WARNING @ Fri, 26 Jun 2020 23:04:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:04:54: #2 You may need to consider one of the other alternative d(s): 2,46,562,567 WARNING @ Fri, 26 Jun 2020 23:04:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:04:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:04:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:05:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:05:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:05:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.10_summits.bed INFO @ Fri, 26 Jun 2020 23:05:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:05:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494839/SRX494839.20_summits.bed INFO @ Fri, 26 Jun 2020 23:05:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 1 millis CompletedMACS2peakCalling