Job ID = 6507946 SRX = SRX495106 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:48:42 prefetch.2.10.7: 1) Downloading 'SRR1198638'... 2020-06-26T13:48:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:50:58 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:50:58 prefetch.2.10.7: 1) 'SRR1198638' was downloaded successfully Read 23003577 spots for SRR1198638/SRR1198638.sra Written 23003577 spots for SRR1198638/SRR1198638.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: 00:05:26 23003577 reads; of these: 23003577 (100.00%) were unpaired; of these: 1606969 (6.99%) aligned 0 times 17616217 (76.58%) aligned exactly 1 time 3780391 (16.43%) aligned >1 times 93.01% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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 12 files... [bam_rmdupse_core] 13810909 / 21396608 = 0.6455 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 23:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.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 23:01:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:01:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:01:51: 1000000 INFO @ Fri, 26 Jun 2020 23:01:57: 2000000 INFO @ Fri, 26 Jun 2020 23:02:02: 3000000 INFO @ Fri, 26 Jun 2020 23:02:08: 4000000 INFO @ Fri, 26 Jun 2020 23:02:13: 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 23:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.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 23:02:16: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:02:16: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:02:19: 6000000 INFO @ Fri, 26 Jun 2020 23:02:23: 1000000 INFO @ Fri, 26 Jun 2020 23:02:25: 7000000 INFO @ Fri, 26 Jun 2020 23:02:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:02:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:02:29: #1 total tags in treatment: 7585699 INFO @ Fri, 26 Jun 2020 23:02:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:02:29: #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 23:02:29: #1 tags after filtering in treatment: 7585699 INFO @ Fri, 26 Jun 2020 23:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:02:29: #1 finished! INFO @ Fri, 26 Jun 2020 23:02:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:02:29: 2000000 INFO @ Fri, 26 Jun 2020 23:02:30: #2 number of paired peaks: 641 WARNING @ Fri, 26 Jun 2020 23:02:30: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Fri, 26 Jun 2020 23:02:30: start model_add_line... INFO @ Fri, 26 Jun 2020 23:02:30: start X-correlation... INFO @ Fri, 26 Jun 2020 23:02:30: end of X-cor INFO @ Fri, 26 Jun 2020 23:02:30: #2 finished! INFO @ Fri, 26 Jun 2020 23:02:30: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 23:02:30: #2 alternative fragment length(s) may be 2,47 bps INFO @ Fri, 26 Jun 2020 23:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.05_model.r WARNING @ Fri, 26 Jun 2020 23:02:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:02:30: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Fri, 26 Jun 2020 23:02:30: #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 23:02:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:02:36: 3000000 INFO @ Fri, 26 Jun 2020 23:02:42: 4000000 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 23:02:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.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 23:02:46: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:02:46: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:02:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:02:48: 5000000 INFO @ Fri, 26 Jun 2020 23:02:52: 1000000 INFO @ Fri, 26 Jun 2020 23:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:02:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:02:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.05_summits.bed INFO @ Fri, 26 Jun 2020 23:02:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (845 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:02:55: 6000000 INFO @ Fri, 26 Jun 2020 23:02:57: 2000000 INFO @ Fri, 26 Jun 2020 23:03:02: 7000000 INFO @ Fri, 26 Jun 2020 23:03:03: 3000000 INFO @ Fri, 26 Jun 2020 23:03:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:03:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:03:05: #1 total tags in treatment: 7585699 INFO @ Fri, 26 Jun 2020 23:03:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:03:05: #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 23:03:05: #1 tags after filtering in treatment: 7585699 INFO @ Fri, 26 Jun 2020 23:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:03:05: #1 finished! INFO @ Fri, 26 Jun 2020 23:03:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:03:06: #2 number of paired peaks: 641 WARNING @ Fri, 26 Jun 2020 23:03:06: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Fri, 26 Jun 2020 23:03:06: start model_add_line... INFO @ Fri, 26 Jun 2020 23:03:06: start X-correlation... INFO @ Fri, 26 Jun 2020 23:03:06: end of X-cor INFO @ Fri, 26 Jun 2020 23:03:06: #2 finished! INFO @ Fri, 26 Jun 2020 23:03:06: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 23:03:06: #2 alternative fragment length(s) may be 2,47 bps INFO @ Fri, 26 Jun 2020 23:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.10_model.r WARNING @ Fri, 26 Jun 2020 23:03:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:03:06: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Fri, 26 Jun 2020 23:03:06: #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 23:03:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:03:09: 4000000 INFO @ Fri, 26 Jun 2020 23:03:14: 5000000 INFO @ Fri, 26 Jun 2020 23:03:19: 6000000 INFO @ Fri, 26 Jun 2020 23:03:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:03:24: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:03:27: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:03:27: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:03:27: #1 total tags in treatment: 7585699 INFO @ Fri, 26 Jun 2020 23:03:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:03:27: #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 23:03:27: #1 tags after filtering in treatment: 7585699 INFO @ Fri, 26 Jun 2020 23:03:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:03:27: #1 finished! INFO @ Fri, 26 Jun 2020 23:03:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:03:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:03:28: #2 number of paired peaks: 641 WARNING @ Fri, 26 Jun 2020 23:03:28: Fewer paired peaks (641) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 641 pairs to build model! INFO @ Fri, 26 Jun 2020 23:03:28: start model_add_line... INFO @ Fri, 26 Jun 2020 23:03:28: start X-correlation... INFO @ Fri, 26 Jun 2020 23:03:28: end of X-cor INFO @ Fri, 26 Jun 2020 23:03:28: #2 finished! INFO @ Fri, 26 Jun 2020 23:03:28: #2 predicted fragment length is 47 bps INFO @ Fri, 26 Jun 2020 23:03:28: #2 alternative fragment length(s) may be 2,47 bps INFO @ Fri, 26 Jun 2020 23:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.20_model.r WARNING @ Fri, 26 Jun 2020 23:03:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:03:28: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Fri, 26 Jun 2020 23:03:28: #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 23:03:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.10_summits.bed INFO @ Fri, 26 Jun 2020 23:03:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (568 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:03:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:03:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:03:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:03:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495106/SRX495106.20_summits.bed INFO @ Fri, 26 Jun 2020 23:03:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 3 millis CompletedMACS2peakCalling