Job ID = 6366752 SRX = SRX2228905 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:02:38 prefetch.2.10.7: 1) Downloading 'SRR4380361'... 2020-06-15T23:02:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:32 prefetch.2.10.7: 'SRR4380361' is valid 2020-06-15T23:03:32 prefetch.2.10.7: 1) 'SRR4380361' was downloaded successfully 2020-06-15T23:03:32 prefetch.2.10.7: 'SRR4380361' has 0 unresolved dependencies Read 16370602 spots for SRR4380361/SRR4380361.sra Written 16370602 spots for SRR4380361/SRR4380361.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: 00:03:49 16370602 reads; of these: 16370602 (100.00%) were unpaired; of these: 120829 (0.74%) aligned 0 times 13576033 (82.93%) aligned exactly 1 time 2673740 (16.33%) aligned >1 times 99.26% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 1407381 / 16249773 = 0.0866 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 08:12:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.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 08:12:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:12:31: 1000000 INFO @ Tue, 16 Jun 2020 08:12:38: 2000000 INFO @ Tue, 16 Jun 2020 08:12:46: 3000000 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 08:12:53: 4000000 INFO @ Tue, 16 Jun 2020 08:12:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.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 08:12:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:12:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:01: 1000000 INFO @ Tue, 16 Jun 2020 08:13:01: 5000000 INFO @ Tue, 16 Jun 2020 08:13:09: 2000000 INFO @ Tue, 16 Jun 2020 08:13:10: 6000000 INFO @ Tue, 16 Jun 2020 08:13:16: 3000000 INFO @ Tue, 16 Jun 2020 08:13:18: 7000000 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 08:13:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.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 08:13:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:24: 4000000 INFO @ Tue, 16 Jun 2020 08:13:27: 8000000 INFO @ Tue, 16 Jun 2020 08:13:32: 1000000 INFO @ Tue, 16 Jun 2020 08:13:32: 5000000 INFO @ Tue, 16 Jun 2020 08:13:35: 9000000 INFO @ Tue, 16 Jun 2020 08:13:40: 2000000 INFO @ Tue, 16 Jun 2020 08:13:40: 6000000 INFO @ Tue, 16 Jun 2020 08:13:44: 10000000 INFO @ Tue, 16 Jun 2020 08:13:49: 3000000 INFO @ Tue, 16 Jun 2020 08:13:49: 7000000 INFO @ Tue, 16 Jun 2020 08:13:53: 11000000 INFO @ Tue, 16 Jun 2020 08:13:57: 4000000 INFO @ Tue, 16 Jun 2020 08:13:57: 8000000 INFO @ Tue, 16 Jun 2020 08:14:02: 12000000 INFO @ Tue, 16 Jun 2020 08:14:05: 5000000 INFO @ Tue, 16 Jun 2020 08:14:05: 9000000 INFO @ Tue, 16 Jun 2020 08:14:11: 13000000 INFO @ Tue, 16 Jun 2020 08:14:14: 6000000 INFO @ Tue, 16 Jun 2020 08:14:14: 10000000 INFO @ Tue, 16 Jun 2020 08:14:20: 14000000 INFO @ Tue, 16 Jun 2020 08:14:22: 7000000 INFO @ Tue, 16 Jun 2020 08:14:22: 11000000 INFO @ Tue, 16 Jun 2020 08:14:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:27: #1 total tags in treatment: 14842392 INFO @ Tue, 16 Jun 2020 08:14:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:27: #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 08:14:28: #1 tags after filtering in treatment: 14842392 INFO @ Tue, 16 Jun 2020 08:14:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:29: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 08:14:29: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:29: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:14:29: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.05_model.r WARNING @ Tue, 16 Jun 2020 08:14:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:29: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:14:29: #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 08:14:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:30: 8000000 INFO @ Tue, 16 Jun 2020 08:14:31: 12000000 INFO @ Tue, 16 Jun 2020 08:14:38: 9000000 INFO @ Tue, 16 Jun 2020 08:14:39: 13000000 INFO @ Tue, 16 Jun 2020 08:14:46: 10000000 INFO @ Tue, 16 Jun 2020 08:14:47: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:53: 11000000 INFO @ Tue, 16 Jun 2020 08:14:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:53: #1 total tags in treatment: 14842392 INFO @ Tue, 16 Jun 2020 08:14:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:53: #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 08:14:53: #1 tags after filtering in treatment: 14842392 INFO @ Tue, 16 Jun 2020 08:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:55: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 08:14:55: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:55: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:55: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:55: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:55: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:55: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:14:55: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.10_model.r WARNING @ Tue, 16 Jun 2020 08:14:55: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:14:55: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:14:55: #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 08:14:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:00: 12000000 INFO @ Tue, 16 Jun 2020 08:15:06: 13000000 INFO @ Tue, 16 Jun 2020 08:15:13: 14000000 INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (649 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:18: #1 total tags in treatment: 14842392 INFO @ Tue, 16 Jun 2020 08:15:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:18: #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 08:15:18: #1 tags after filtering in treatment: 14842392 INFO @ Tue, 16 Jun 2020 08:15:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:19: #2 number of paired peaks: 254 WARNING @ Tue, 16 Jun 2020 08:15:19: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:19: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:15:19: #2 alternative fragment length(s) may be 2,49 bps INFO @ Tue, 16 Jun 2020 08:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.20_model.r WARNING @ Tue, 16 Jun 2020 08:15:19: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:19: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Tue, 16 Jun 2020 08:15:19: #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 08:15:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (413 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228905/SRX2228905.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling