Job ID = 6368561 SRX = SRX5020787 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:31 prefetch.2.10.7: 1) Downloading 'SRR8201410'... 2020-06-16T00:25:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:45 prefetch.2.10.7: 'SRR8201410' is valid 2020-06-16T00:28:45 prefetch.2.10.7: 1) 'SRR8201410' was downloaded successfully 2020-06-16T00:28:45 prefetch.2.10.7: 'SRR8201410' has 0 unresolved dependencies Read 17082672 spots for SRR8201410/SRR8201410.sra Written 17082672 spots for SRR8201410/SRR8201410.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: 00:05:48 17082672 reads; of these: 17082672 (100.00%) were unpaired; of these: 4163382 (24.37%) aligned 0 times 10729550 (62.81%) aligned exactly 1 time 2189740 (12.82%) aligned >1 times 75.63% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 3059907 / 12919290 = 0.2368 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 09:39:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.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 09:39:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:16: 1000000 INFO @ Tue, 16 Jun 2020 09:39:22: 2000000 INFO @ Tue, 16 Jun 2020 09:39:27: 3000000 INFO @ Tue, 16 Jun 2020 09:39:33: 4000000 INFO @ Tue, 16 Jun 2020 09:39:38: 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 09:39:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.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 09:39:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:44: 6000000 INFO @ Tue, 16 Jun 2020 09:39:46: 1000000 INFO @ Tue, 16 Jun 2020 09:39:49: 7000000 INFO @ Tue, 16 Jun 2020 09:39:51: 2000000 INFO @ Tue, 16 Jun 2020 09:39:55: 8000000 INFO @ Tue, 16 Jun 2020 09:39:57: 3000000 INFO @ Tue, 16 Jun 2020 09:40:00: 9000000 INFO @ Tue, 16 Jun 2020 09:40:02: 4000000 INFO @ Tue, 16 Jun 2020 09:40:05: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:40:05: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:40:05: #1 total tags in treatment: 9859383 INFO @ Tue, 16 Jun 2020 09:40:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:05: #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 09:40:05: #1 tags after filtering in treatment: 9859383 INFO @ Tue, 16 Jun 2020 09:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:06: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:40:06: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:06: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:40:06: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 16 Jun 2020 09:40:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.05_model.r WARNING @ Tue, 16 Jun 2020 09:40:06: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:06: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 16 Jun 2020 09:40:06: #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 09:40:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:07: 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 09:40:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.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 09:40:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:13: 6000000 INFO @ Tue, 16 Jun 2020 09:40:16: 1000000 INFO @ Tue, 16 Jun 2020 09:40:18: 7000000 INFO @ Tue, 16 Jun 2020 09:40:22: 2000000 INFO @ Tue, 16 Jun 2020 09:40:23: 8000000 INFO @ Tue, 16 Jun 2020 09:40:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:27: 3000000 INFO @ Tue, 16 Jun 2020 09:40:29: 9000000 INFO @ Tue, 16 Jun 2020 09:40:32: 4000000 INFO @ Tue, 16 Jun 2020 09:40:33: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:40:33: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:40:33: #1 total tags in treatment: 9859383 INFO @ Tue, 16 Jun 2020 09:40:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:33: #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 09:40:33: #1 tags after filtering in treatment: 9859383 INFO @ Tue, 16 Jun 2020 09:40:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:34: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:40:34: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:34: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:40:34: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 16 Jun 2020 09:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.10_model.r WARNING @ Tue, 16 Jun 2020 09:40:34: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:34: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 16 Jun 2020 09:40:34: #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 09:40:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.05_summits.bed INFO @ Tue, 16 Jun 2020 09:40:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1080 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:37: 5000000 INFO @ Tue, 16 Jun 2020 09:40:43: 6000000 INFO @ Tue, 16 Jun 2020 09:40:48: 7000000 INFO @ Tue, 16 Jun 2020 09:40:53: 8000000 INFO @ Tue, 16 Jun 2020 09:40:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:58: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:41:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:41:03: #1 total tags in treatment: 9859383 INFO @ Tue, 16 Jun 2020 09:41:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:03: #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 09:41:03: #1 tags after filtering in treatment: 9859383 INFO @ Tue, 16 Jun 2020 09:41:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (572 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:03: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:41:03: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:04: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:41:04: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 16 Jun 2020 09:41:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.20_model.r WARNING @ Tue, 16 Jun 2020 09:41:04: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:04: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 16 Jun 2020 09:41:04: #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 09:41:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020787/SRX5020787.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 1 millis CompletedMACS2peakCalling