Job ID = 6368963 SRX = SRX796307 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T01:00:26 prefetch.2.10.7: 1) Downloading 'SRR1693482'... 2020-06-16T01:00:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T01:01:38 prefetch.2.10.7: HTTPS download succeed 2020-06-16T01:01:39 prefetch.2.10.7: 'SRR1693482' is valid 2020-06-16T01:01:39 prefetch.2.10.7: 1) 'SRR1693482' was downloaded successfully Read 17254347 spots for SRR1693482/SRR1693482.sra Written 17254347 spots for SRR1693482/SRR1693482.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: 00:03:19 17254347 reads; of these: 17254347 (100.00%) were unpaired; of these: 242862 (1.41%) aligned 0 times 13600099 (78.82%) aligned exactly 1 time 3411386 (19.77%) aligned >1 times 98.59% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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] 13321979 / 17011485 = 0.7831 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 10:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.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 10:09:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:22: 1000000 INFO @ Tue, 16 Jun 2020 10:09:29: 2000000 INFO @ Tue, 16 Jun 2020 10:09:35: 3000000 INFO @ Tue, 16 Jun 2020 10:09:40: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 10:09:40: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 10:09:40: #1 total tags in treatment: 3689506 INFO @ Tue, 16 Jun 2020 10:09:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:09:40: #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 10:09:40: #1 tags after filtering in treatment: 3689506 INFO @ Tue, 16 Jun 2020 10:09:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:09:40: #1 finished! INFO @ Tue, 16 Jun 2020 10:09:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:09:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:09:40: #2 number of paired peaks: 718 WARNING @ Tue, 16 Jun 2020 10:09:40: Fewer paired peaks (718) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 718 pairs to build model! INFO @ Tue, 16 Jun 2020 10:09:40: start model_add_line... INFO @ Tue, 16 Jun 2020 10:09:40: start X-correlation... INFO @ Tue, 16 Jun 2020 10:09:40: end of X-cor INFO @ Tue, 16 Jun 2020 10:09:40: #2 finished! INFO @ Tue, 16 Jun 2020 10:09:40: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 10:09:40: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 16 Jun 2020 10:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.05_model.r WARNING @ Tue, 16 Jun 2020 10:09:40: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:09:40: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 16 Jun 2020 10:09:40: #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 10:09:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:09:40: #3 Pre-compute pvalue-qvalue table... 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 10:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.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 10:09:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.05_summits.bed INFO @ Tue, 16 Jun 2020 10:09:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1719 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:09:53: 1000000 INFO @ Tue, 16 Jun 2020 10:10:00: 2000000 INFO @ Tue, 16 Jun 2020 10:10:08: 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 10:10:13: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 10:10:13: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 10:10:13: #1 total tags in treatment: 3689506 INFO @ Tue, 16 Jun 2020 10:10:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:10:13: #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 10:10:13: #1 tags after filtering in treatment: 3689506 INFO @ Tue, 16 Jun 2020 10:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:10:13: #1 finished! INFO @ Tue, 16 Jun 2020 10:10:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:10:13: #2 number of paired peaks: 718 WARNING @ Tue, 16 Jun 2020 10:10:13: Fewer paired peaks (718) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 718 pairs to build model! INFO @ Tue, 16 Jun 2020 10:10:13: start model_add_line... INFO @ Tue, 16 Jun 2020 10:10:13: start X-correlation... INFO @ Tue, 16 Jun 2020 10:10:13: end of X-cor INFO @ Tue, 16 Jun 2020 10:10:13: #2 finished! INFO @ Tue, 16 Jun 2020 10:10:13: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 10:10:13: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 16 Jun 2020 10:10:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.10_model.r WARNING @ Tue, 16 Jun 2020 10:10:13: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:10:13: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 16 Jun 2020 10:10:13: #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 10:10:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:10:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.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 10:10:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:10:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:10:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:10:23: 1000000 INFO @ Tue, 16 Jun 2020 10:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.10_summits.bed INFO @ Tue, 16 Jun 2020 10:10:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (714 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:10:31: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:10:38: 3000000 INFO @ Tue, 16 Jun 2020 10:10:43: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 10:10:43: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 10:10:43: #1 total tags in treatment: 3689506 INFO @ Tue, 16 Jun 2020 10:10:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:10:43: #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 10:10:43: #1 tags after filtering in treatment: 3689506 INFO @ Tue, 16 Jun 2020 10:10:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:10:43: #1 finished! INFO @ Tue, 16 Jun 2020 10:10:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:10:43: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:10:44: #2 number of paired peaks: 718 WARNING @ Tue, 16 Jun 2020 10:10:44: Fewer paired peaks (718) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 718 pairs to build model! INFO @ Tue, 16 Jun 2020 10:10:44: start model_add_line... INFO @ Tue, 16 Jun 2020 10:10:44: start X-correlation... INFO @ Tue, 16 Jun 2020 10:10:44: end of X-cor INFO @ Tue, 16 Jun 2020 10:10:44: #2 finished! INFO @ Tue, 16 Jun 2020 10:10:44: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 10:10:44: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 16 Jun 2020 10:10:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.20_model.r WARNING @ Tue, 16 Jun 2020 10:10:44: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:10:44: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 16 Jun 2020 10:10:44: #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 10:10:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:10:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:10:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:10:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:10:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:10:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX796307/SRX796307.20_summits.bed INFO @ Tue, 16 Jun 2020 10:10:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 1 millis CompletedMACS2peakCalling