Job ID = 6368304 SRX = SRX494987 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:01:30 prefetch.2.10.7: 1) Downloading 'SRR1198519'... 2020-06-16T00:01:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:48 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:49 prefetch.2.10.7: 'SRR1198519' is valid 2020-06-16T00:02:49 prefetch.2.10.7: 1) 'SRR1198519' was downloaded successfully Read 15351480 spots for SRR1198519/SRR1198519.sra Written 15351480 spots for SRR1198519/SRR1198519.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: 00:02:46 15351480 reads; of these: 15351480 (100.00%) were unpaired; of these: 137953 (0.90%) aligned 0 times 12385296 (80.68%) aligned exactly 1 time 2828231 (18.42%) aligned >1 times 99.10% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 2342769 / 15213527 = 0.1540 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 09:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.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 09:10:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:39: 1000000 INFO @ Tue, 16 Jun 2020 09:10:44: 2000000 INFO @ Tue, 16 Jun 2020 09:10:49: 3000000 INFO @ Tue, 16 Jun 2020 09:10:54: 4000000 INFO @ Tue, 16 Jun 2020 09:10:59: 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 09:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.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 09:11:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:04: 6000000 INFO @ Tue, 16 Jun 2020 09:11:09: 7000000 INFO @ Tue, 16 Jun 2020 09:11:09: 1000000 INFO @ Tue, 16 Jun 2020 09:11:14: 2000000 INFO @ Tue, 16 Jun 2020 09:11:14: 8000000 INFO @ Tue, 16 Jun 2020 09:11:19: 3000000 INFO @ Tue, 16 Jun 2020 09:11:19: 9000000 INFO @ Tue, 16 Jun 2020 09:11:24: 10000000 INFO @ Tue, 16 Jun 2020 09:11:24: 4000000 INFO @ Tue, 16 Jun 2020 09:11:29: 11000000 INFO @ Tue, 16 Jun 2020 09:11:30: 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 09:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.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 09:11:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:34: 12000000 INFO @ Tue, 16 Jun 2020 09:11:35: 6000000 INFO @ Tue, 16 Jun 2020 09:11:38: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:11:38: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:11:38: #1 total tags in treatment: 12870758 INFO @ Tue, 16 Jun 2020 09:11:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:38: #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 09:11:39: #1 tags after filtering in treatment: 12870758 INFO @ Tue, 16 Jun 2020 09:11:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:40: #2 number of paired peaks: 367 WARNING @ Tue, 16 Jun 2020 09:11:40: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:40: 1000000 INFO @ Tue, 16 Jun 2020 09:11:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:40: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:11:40: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 09:11:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:40: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:40: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 09:11:40: #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 09:11:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:41: 7000000 INFO @ Tue, 16 Jun 2020 09:11:46: 2000000 INFO @ Tue, 16 Jun 2020 09:11:47: 8000000 INFO @ Tue, 16 Jun 2020 09:11:51: 3000000 INFO @ Tue, 16 Jun 2020 09:11:53: 9000000 INFO @ Tue, 16 Jun 2020 09:11:57: 4000000 INFO @ Tue, 16 Jun 2020 09:11:59: 10000000 INFO @ Tue, 16 Jun 2020 09:12:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:03: 5000000 INFO @ Tue, 16 Jun 2020 09:12:05: 11000000 INFO @ Tue, 16 Jun 2020 09:12:09: 6000000 INFO @ Tue, 16 Jun 2020 09:12:11: 12000000 INFO @ Tue, 16 Jun 2020 09:12:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2149 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:15: 7000000 INFO @ Tue, 16 Jun 2020 09:12:17: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:17: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:17: #1 total tags in treatment: 12870758 INFO @ Tue, 16 Jun 2020 09:12:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:17: #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 09:12:17: #1 tags after filtering in treatment: 12870758 INFO @ Tue, 16 Jun 2020 09:12:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:18: #2 number of paired peaks: 367 WARNING @ Tue, 16 Jun 2020 09:12:18: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:18: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:12:18: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 09:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:18: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:18: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 09:12:18: #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 09:12:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:21: 8000000 INFO @ Tue, 16 Jun 2020 09:12:26: 9000000 INFO @ Tue, 16 Jun 2020 09:12:32: 10000000 INFO @ Tue, 16 Jun 2020 09:12:37: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:43: 12000000 INFO @ Tue, 16 Jun 2020 09:12:48: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:48: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:48: #1 total tags in treatment: 12870758 INFO @ Tue, 16 Jun 2020 09:12:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:48: #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 09:12:48: #1 tags after filtering in treatment: 12870758 INFO @ Tue, 16 Jun 2020 09:12:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:49: #2 number of paired peaks: 367 WARNING @ Tue, 16 Jun 2020 09:12:49: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:49: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:12:49: #2 alternative fragment length(s) may be 2,41 bps INFO @ Tue, 16 Jun 2020 09:12:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:49: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:49: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Tue, 16 Jun 2020 09:12:49: #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 09:12:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (595 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494987/SRX494987.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (186 records, 4 fields): 2 millis CompletedMACS2peakCalling