Job ID = 6497568 SRX = SRX743651 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:14:44 prefetch.2.10.7: 1) Downloading 'SRR1630866'... 2020-06-25T22:14:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:15:54 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:15:54 prefetch.2.10.7: 'SRR1630866' is valid 2020-06-25T22:15:54 prefetch.2.10.7: 1) 'SRR1630866' was downloaded successfully Read 10326979 spots for SRR1630866/SRR1630866.sra Written 10326979 spots for SRR1630866/SRR1630866.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: 00:03:00 10326979 reads; of these: 10326979 (100.00%) were unpaired; of these: 121133 (1.17%) aligned 0 times 8594225 (83.22%) aligned exactly 1 time 1611621 (15.61%) aligned >1 times 98.83% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 1288071 / 10205846 = 0.1262 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 07:22:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.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 07:22:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:28: 1000000 INFO @ Fri, 26 Jun 2020 07:22:33: 2000000 INFO @ Fri, 26 Jun 2020 07:22:38: 3000000 INFO @ Fri, 26 Jun 2020 07:22:43: 4000000 INFO @ Fri, 26 Jun 2020 07:22:49: 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 @ Fri, 26 Jun 2020 07:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.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 07:22:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:54: 6000000 INFO @ Fri, 26 Jun 2020 07:22:58: 1000000 INFO @ Fri, 26 Jun 2020 07:23:00: 7000000 INFO @ Fri, 26 Jun 2020 07:23:03: 2000000 INFO @ Fri, 26 Jun 2020 07:23:05: 8000000 INFO @ Fri, 26 Jun 2020 07:23:09: 3000000 INFO @ Fri, 26 Jun 2020 07:23:10: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:23:10: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:23:10: #1 total tags in treatment: 8917775 INFO @ Fri, 26 Jun 2020 07:23:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:23:10: #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 07:23:11: #1 tags after filtering in treatment: 8917775 INFO @ Fri, 26 Jun 2020 07:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:23:11: #1 finished! INFO @ Fri, 26 Jun 2020 07:23:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:23:11: #2 number of paired peaks: 204 WARNING @ Fri, 26 Jun 2020 07:23:11: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Fri, 26 Jun 2020 07:23:11: start model_add_line... INFO @ Fri, 26 Jun 2020 07:23:11: start X-correlation... INFO @ Fri, 26 Jun 2020 07:23:11: end of X-cor INFO @ Fri, 26 Jun 2020 07:23:11: #2 finished! INFO @ Fri, 26 Jun 2020 07:23:11: #2 predicted fragment length is 55 bps INFO @ Fri, 26 Jun 2020 07:23:11: #2 alternative fragment length(s) may be 2,55,504,532,594 bps INFO @ Fri, 26 Jun 2020 07:23:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.05_model.r INFO @ Fri, 26 Jun 2020 07:23:14: 4000000 WARNING @ Fri, 26 Jun 2020 07:23:14: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:23:14: #2 You may need to consider one of the other alternative d(s): 2,55,504,532,594 WARNING @ Fri, 26 Jun 2020 07:23:14: #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 07:23:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:23:20: 5000000 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 07:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.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 07:23:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:23:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:23:25: 6000000 INFO @ Fri, 26 Jun 2020 07:23:28: 1000000 INFO @ Fri, 26 Jun 2020 07:23:31: 7000000 INFO @ Fri, 26 Jun 2020 07:23:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:23:34: 2000000 INFO @ Fri, 26 Jun 2020 07:23:37: 8000000 INFO @ Fri, 26 Jun 2020 07:23:40: 3000000 INFO @ Fri, 26 Jun 2020 07:23:42: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:23:42: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:23:42: #1 total tags in treatment: 8917775 INFO @ Fri, 26 Jun 2020 07:23:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:23:42: #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 07:23:42: #1 tags after filtering in treatment: 8917775 INFO @ Fri, 26 Jun 2020 07:23:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:23:42: #1 finished! INFO @ Fri, 26 Jun 2020 07:23:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:23:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:23:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:23:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:23:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.05_summits.bed INFO @ Fri, 26 Jun 2020 07:23:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (524 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:23:43: #2 number of paired peaks: 204 WARNING @ Fri, 26 Jun 2020 07:23:43: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Fri, 26 Jun 2020 07:23:43: start model_add_line... INFO @ Fri, 26 Jun 2020 07:23:43: start X-correlation... INFO @ Fri, 26 Jun 2020 07:23:43: end of X-cor INFO @ Fri, 26 Jun 2020 07:23:43: #2 finished! INFO @ Fri, 26 Jun 2020 07:23:43: #2 predicted fragment length is 55 bps INFO @ Fri, 26 Jun 2020 07:23:43: #2 alternative fragment length(s) may be 2,55,504,532,594 bps INFO @ Fri, 26 Jun 2020 07:23:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.10_model.r WARNING @ Fri, 26 Jun 2020 07:23:43: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:23:43: #2 You may need to consider one of the other alternative d(s): 2,55,504,532,594 WARNING @ Fri, 26 Jun 2020 07:23:43: #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 07:23:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:23:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:23:45: 4000000 INFO @ Fri, 26 Jun 2020 07:23:51: 5000000 INFO @ Fri, 26 Jun 2020 07:23:57: 6000000 INFO @ Fri, 26 Jun 2020 07:24:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:24:02: 7000000 INFO @ Fri, 26 Jun 2020 07:24:08: 8000000 INFO @ Fri, 26 Jun 2020 07:24:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:24:13: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 07:24:13: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 07:24:13: #1 total tags in treatment: 8917775 INFO @ Fri, 26 Jun 2020 07:24:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:24:13: #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 07:24:13: #1 tags after filtering in treatment: 8917775 INFO @ Fri, 26 Jun 2020 07:24:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:24:13: #1 finished! INFO @ Fri, 26 Jun 2020 07:24:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:24:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:24:14: #2 number of paired peaks: 204 WARNING @ Fri, 26 Jun 2020 07:24:14: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Fri, 26 Jun 2020 07:24:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:24:14: start X-correlation... INFO @ Fri, 26 Jun 2020 07:24:14: end of X-cor INFO @ Fri, 26 Jun 2020 07:24:14: #2 finished! INFO @ Fri, 26 Jun 2020 07:24:14: #2 predicted fragment length is 55 bps INFO @ Fri, 26 Jun 2020 07:24:14: #2 alternative fragment length(s) may be 2,55,504,532,594 bps INFO @ Fri, 26 Jun 2020 07:24:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.20_model.r BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.10_peaks.narrowPeak WARNING @ Fri, 26 Jun 2020 07:24:43: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:24:43: #2 You may need to consider one of the other alternative d(s): 2,55,504,532,594 WARNING @ Fri, 26 Jun 2020 07:24:43: #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 07:24:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.10_summits.bed BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:24:43: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (283 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:25:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX743651/SRX743651.20_summits.bed INFO @ Fri, 26 Jun 2020 07:25:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (82 records, 4 fields): 1 millis CompletedMACS2peakCalling