Job ID = 6368629 SRX = SRX5073497 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:20 prefetch.2.10.7: 1) Downloading 'SRR8255717'... 2020-06-16T00:14:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:39 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:40 prefetch.2.10.7: 'SRR8255717' is valid 2020-06-16T00:16:40 prefetch.2.10.7: 1) 'SRR8255717' was downloaded successfully 2020-06-16T00:16:40 prefetch.2.10.7: 'SRR8255717' has 0 unresolved dependencies Read 25794530 spots for SRR8255717/SRR8255717.sra Written 25794530 spots for SRR8255717/SRR8255717.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: 00:05:16 25794530 reads; of these: 25794530 (100.00%) were unpaired; of these: 1592881 (6.18%) aligned 0 times 20556345 (79.69%) aligned exactly 1 time 3645304 (14.13%) aligned >1 times 93.82% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 7592614 / 24201649 = 0.3137 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 09:26:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.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 09:26:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:04: 1000000 INFO @ Tue, 16 Jun 2020 09:27:08: 2000000 INFO @ Tue, 16 Jun 2020 09:27:13: 3000000 INFO @ Tue, 16 Jun 2020 09:27:18: 4000000 INFO @ Tue, 16 Jun 2020 09:27:23: 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 09:27:27: 6000000 INFO @ Tue, 16 Jun 2020 09:27:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.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 09:27:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:32: 7000000 INFO @ Tue, 16 Jun 2020 09:27:34: 1000000 INFO @ Tue, 16 Jun 2020 09:27:37: 8000000 INFO @ Tue, 16 Jun 2020 09:27:39: 2000000 INFO @ Tue, 16 Jun 2020 09:27:42: 9000000 INFO @ Tue, 16 Jun 2020 09:27:44: 3000000 INFO @ Tue, 16 Jun 2020 09:27:47: 10000000 INFO @ Tue, 16 Jun 2020 09:27:49: 4000000 INFO @ Tue, 16 Jun 2020 09:27:52: 11000000 INFO @ Tue, 16 Jun 2020 09:27:54: 5000000 INFO @ Tue, 16 Jun 2020 09:27:57: 12000000 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 09:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.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 09:27:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:59: 6000000 INFO @ Tue, 16 Jun 2020 09:28:02: 13000000 INFO @ Tue, 16 Jun 2020 09:28:04: 1000000 INFO @ Tue, 16 Jun 2020 09:28:05: 7000000 INFO @ Tue, 16 Jun 2020 09:28:07: 14000000 INFO @ Tue, 16 Jun 2020 09:28:09: 2000000 INFO @ Tue, 16 Jun 2020 09:28:10: 8000000 INFO @ Tue, 16 Jun 2020 09:28:12: 15000000 INFO @ Tue, 16 Jun 2020 09:28:14: 3000000 INFO @ Tue, 16 Jun 2020 09:28:15: 9000000 INFO @ Tue, 16 Jun 2020 09:28:17: 16000000 INFO @ Tue, 16 Jun 2020 09:28:20: 4000000 INFO @ Tue, 16 Jun 2020 09:28:20: 10000000 INFO @ Tue, 16 Jun 2020 09:28:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:28:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:28:20: #1 total tags in treatment: 16609035 INFO @ Tue, 16 Jun 2020 09:28:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:20: #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 09:28:21: #1 tags after filtering in treatment: 16609035 INFO @ Tue, 16 Jun 2020 09:28:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:22: #2 number of paired peaks: 173 WARNING @ Tue, 16 Jun 2020 09:28:22: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:22: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 09:28:22: #2 alternative fragment length(s) may be 1,40,64 bps INFO @ Tue, 16 Jun 2020 09:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.05_model.r WARNING @ Tue, 16 Jun 2020 09:28:22: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:22: #2 You may need to consider one of the other alternative d(s): 1,40,64 WARNING @ Tue, 16 Jun 2020 09:28:22: #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 09:28:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:25: 5000000 INFO @ Tue, 16 Jun 2020 09:28:25: 11000000 INFO @ Tue, 16 Jun 2020 09:28:30: 6000000 INFO @ Tue, 16 Jun 2020 09:28:30: 12000000 INFO @ Tue, 16 Jun 2020 09:28:35: 7000000 INFO @ Tue, 16 Jun 2020 09:28:36: 13000000 INFO @ Tue, 16 Jun 2020 09:28:40: 8000000 INFO @ Tue, 16 Jun 2020 09:28:41: 14000000 INFO @ Tue, 16 Jun 2020 09:28:45: 9000000 INFO @ Tue, 16 Jun 2020 09:28:46: 15000000 INFO @ Tue, 16 Jun 2020 09:28:50: 10000000 INFO @ Tue, 16 Jun 2020 09:28:51: 16000000 INFO @ Tue, 16 Jun 2020 09:28:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:28:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:28:54: #1 total tags in treatment: 16609035 INFO @ Tue, 16 Jun 2020 09:28:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:54: #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 09:28:55: #1 tags after filtering in treatment: 16609035 INFO @ Tue, 16 Jun 2020 09:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:55: 11000000 INFO @ Tue, 16 Jun 2020 09:28:56: #2 number of paired peaks: 173 WARNING @ Tue, 16 Jun 2020 09:28:56: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 16 Jun 2020 09:28:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:56: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 09:28:56: #2 alternative fragment length(s) may be 1,40,64 bps INFO @ Tue, 16 Jun 2020 09:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.10_model.r WARNING @ Tue, 16 Jun 2020 09:28:56: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:28:56: #2 You may need to consider one of the other alternative d(s): 1,40,64 WARNING @ Tue, 16 Jun 2020 09:28:56: #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 09:28:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:00: 12000000 INFO @ Tue, 16 Jun 2020 09:29:05: 13000000 INFO @ Tue, 16 Jun 2020 09:29:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1543 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:10: 14000000 INFO @ Tue, 16 Jun 2020 09:29:15: 15000000 INFO @ Tue, 16 Jun 2020 09:29:20: 16000000 INFO @ Tue, 16 Jun 2020 09:29:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:29:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:29:23: #1 total tags in treatment: 16609035 INFO @ Tue, 16 Jun 2020 09:29:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:23: #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 09:29:23: #1 tags after filtering in treatment: 16609035 INFO @ Tue, 16 Jun 2020 09:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:24: #2 number of paired peaks: 173 WARNING @ Tue, 16 Jun 2020 09:29:24: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:24: #2 predicted fragment length is 64 bps INFO @ Tue, 16 Jun 2020 09:29:24: #2 alternative fragment length(s) may be 1,40,64 bps INFO @ Tue, 16 Jun 2020 09:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.20_model.r WARNING @ Tue, 16 Jun 2020 09:29:24: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:24: #2 You may need to consider one of the other alternative d(s): 1,40,64 WARNING @ Tue, 16 Jun 2020 09:29:24: #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 09:29:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (435 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073497/SRX5073497.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (131 records, 4 fields): 1 millis CompletedMACS2peakCalling