Job ID = 6366631 SRX = SRX2144178 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:41:44 prefetch.2.10.7: 1) Downloading 'SRR4188782'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:27 prefetch.2.10.7: 'SRR4188782' is valid 2020-06-15T23:43:27 prefetch.2.10.7: 1) 'SRR4188782' was downloaded successfully Read 8786701 spots for SRR4188782/SRR4188782.sra Written 8786701 spots for SRR4188782/SRR4188782.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: 00:01:54 8786701 reads; of these: 8786701 (100.00%) were unpaired; of these: 691594 (7.87%) aligned 0 times 6537141 (74.40%) aligned exactly 1 time 1557966 (17.73%) aligned >1 times 92.13% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 567855 / 8095107 = 0.0701 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 08:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.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 08:49:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:14: 1000000 INFO @ Tue, 16 Jun 2020 08:49:19: 2000000 INFO @ Tue, 16 Jun 2020 08:49:24: 3000000 INFO @ Tue, 16 Jun 2020 08:49:30: 4000000 INFO @ Tue, 16 Jun 2020 08:49:35: 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 @ Tue, 16 Jun 2020 08:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.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 08:49:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:40: 6000000 INFO @ Tue, 16 Jun 2020 08:49:44: 1000000 INFO @ Tue, 16 Jun 2020 08:49:46: 7000000 INFO @ Tue, 16 Jun 2020 08:49:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:49:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:49:49: #1 total tags in treatment: 7527252 INFO @ Tue, 16 Jun 2020 08:49:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:49: #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 08:49:49: #1 tags after filtering in treatment: 7527252 INFO @ Tue, 16 Jun 2020 08:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:49: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:49: #2 number of paired peaks: 412 WARNING @ Tue, 16 Jun 2020 08:49:49: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:50: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:50: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:50: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:50: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:49:50: #2 alternative fragment length(s) may be 4,47,522 bps INFO @ Tue, 16 Jun 2020 08:49:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.05_model.r WARNING @ Tue, 16 Jun 2020 08:49:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:50: #2 You may need to consider one of the other alternative d(s): 4,47,522 WARNING @ Tue, 16 Jun 2020 08:49:50: #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 08:49:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:50: 2000000 INFO @ Tue, 16 Jun 2020 08:49:55: 3000000 INFO @ Tue, 16 Jun 2020 08:50:00: 4000000 INFO @ Tue, 16 Jun 2020 08:50:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:05: 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 @ Tue, 16 Jun 2020 08:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.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 08:50:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:11: 6000000 INFO @ Tue, 16 Jun 2020 08:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (643 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:16: 1000000 INFO @ Tue, 16 Jun 2020 08:50:16: 7000000 INFO @ Tue, 16 Jun 2020 08:50:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:19: #1 total tags in treatment: 7527252 INFO @ Tue, 16 Jun 2020 08:50:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:19: #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 08:50:19: #1 tags after filtering in treatment: 7527252 INFO @ Tue, 16 Jun 2020 08:50:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:20: #2 number of paired peaks: 412 WARNING @ Tue, 16 Jun 2020 08:50:20: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:20: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:50:20: #2 alternative fragment length(s) may be 4,47,522 bps INFO @ Tue, 16 Jun 2020 08:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:20: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:20: #2 You may need to consider one of the other alternative d(s): 4,47,522 WARNING @ Tue, 16 Jun 2020 08:50:20: #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 08:50:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:23: 2000000 INFO @ Tue, 16 Jun 2020 08:50:29: 3000000 INFO @ Tue, 16 Jun 2020 08:50:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:36: 4000000 INFO @ Tue, 16 Jun 2020 08:50:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (395 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:43: 5000000 INFO @ Tue, 16 Jun 2020 08:50:49: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:56: 7000000 INFO @ Tue, 16 Jun 2020 08:51:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:00: #1 total tags in treatment: 7527252 INFO @ Tue, 16 Jun 2020 08:51:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:00: #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 08:51:00: #1 tags after filtering in treatment: 7527252 INFO @ Tue, 16 Jun 2020 08:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:00: #2 number of paired peaks: 412 WARNING @ Tue, 16 Jun 2020 08:51:00: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:01: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:51:01: #2 alternative fragment length(s) may be 4,47,522 bps INFO @ Tue, 16 Jun 2020 08:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:01: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:01: #2 You may need to consider one of the other alternative d(s): 4,47,522 WARNING @ Tue, 16 Jun 2020 08:51:01: #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 08:51:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2144178/SRX2144178.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 1 millis CompletedMACS2peakCalling