Job ID = 6368040 SRX = SRX466503 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:05 prefetch.2.10.7: 1) Downloading 'SRR1163569'... 2020-06-15T23:58:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:50 prefetch.2.10.7: 1) 'SRR1163569' was downloaded successfully Read 21509609 spots for SRR1163569/SRR1163569.sra Written 21509609 spots for SRR1163569/SRR1163569.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: 00:03:59 21509609 reads; of these: 21509609 (100.00%) were unpaired; of these: 255394 (1.19%) aligned 0 times 17821593 (82.85%) aligned exactly 1 time 3432622 (15.96%) aligned >1 times 98.81% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 3667042 / 21254215 = 0.1725 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 09:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.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 09:11:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:48: 1000000 INFO @ Tue, 16 Jun 2020 09:11:53: 2000000 INFO @ Tue, 16 Jun 2020 09:11:57: 3000000 INFO @ Tue, 16 Jun 2020 09:12:02: 4000000 INFO @ Tue, 16 Jun 2020 09:12:07: 5000000 INFO @ Tue, 16 Jun 2020 09:12:11: 6000000 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 09:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.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 09:12:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:16: 7000000 INFO @ Tue, 16 Jun 2020 09:12:18: 1000000 INFO @ Tue, 16 Jun 2020 09:12:21: 8000000 INFO @ Tue, 16 Jun 2020 09:12:23: 2000000 INFO @ Tue, 16 Jun 2020 09:12:26: 9000000 INFO @ Tue, 16 Jun 2020 09:12:27: 3000000 INFO @ Tue, 16 Jun 2020 09:12:30: 10000000 INFO @ Tue, 16 Jun 2020 09:12:32: 4000000 INFO @ Tue, 16 Jun 2020 09:12:35: 11000000 INFO @ Tue, 16 Jun 2020 09:12:37: 5000000 INFO @ Tue, 16 Jun 2020 09:12:40: 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 09:12:42: 6000000 INFO @ Tue, 16 Jun 2020 09:12:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.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 09:12:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:45: 13000000 INFO @ Tue, 16 Jun 2020 09:12:46: 7000000 INFO @ Tue, 16 Jun 2020 09:12:48: 1000000 INFO @ Tue, 16 Jun 2020 09:12:49: 14000000 INFO @ Tue, 16 Jun 2020 09:12:51: 8000000 INFO @ Tue, 16 Jun 2020 09:12:53: 2000000 INFO @ Tue, 16 Jun 2020 09:12:54: 15000000 INFO @ Tue, 16 Jun 2020 09:12:56: 9000000 INFO @ Tue, 16 Jun 2020 09:12:58: 3000000 INFO @ Tue, 16 Jun 2020 09:12:59: 16000000 INFO @ Tue, 16 Jun 2020 09:13:01: 10000000 INFO @ Tue, 16 Jun 2020 09:13:02: 4000000 INFO @ Tue, 16 Jun 2020 09:13:04: 17000000 INFO @ Tue, 16 Jun 2020 09:13:06: 11000000 INFO @ Tue, 16 Jun 2020 09:13:07: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:07: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:07: #1 total tags in treatment: 17587173 INFO @ Tue, 16 Jun 2020 09:13:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:07: #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 09:13:07: 5000000 INFO @ Tue, 16 Jun 2020 09:13:07: #1 tags after filtering in treatment: 17587173 INFO @ Tue, 16 Jun 2020 09:13:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:09: #2 number of paired peaks: 213 WARNING @ Tue, 16 Jun 2020 09:13:09: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:09: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:13:09: #2 alternative fragment length(s) may be 1,37,541,576 bps INFO @ Tue, 16 Jun 2020 09:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.05_model.r WARNING @ Tue, 16 Jun 2020 09:13:09: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:09: #2 You may need to consider one of the other alternative d(s): 1,37,541,576 WARNING @ Tue, 16 Jun 2020 09:13:09: #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 09:13:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:11: 12000000 INFO @ Tue, 16 Jun 2020 09:13:12: 6000000 INFO @ Tue, 16 Jun 2020 09:13:15: 13000000 INFO @ Tue, 16 Jun 2020 09:13:17: 7000000 INFO @ Tue, 16 Jun 2020 09:13:20: 14000000 INFO @ Tue, 16 Jun 2020 09:13:21: 8000000 INFO @ Tue, 16 Jun 2020 09:13:25: 15000000 INFO @ Tue, 16 Jun 2020 09:13:26: 9000000 INFO @ Tue, 16 Jun 2020 09:13:30: 16000000 INFO @ Tue, 16 Jun 2020 09:13:31: 10000000 INFO @ Tue, 16 Jun 2020 09:13:35: 17000000 INFO @ Tue, 16 Jun 2020 09:13:36: 11000000 INFO @ Tue, 16 Jun 2020 09:13:38: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:38: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:38: #1 total tags in treatment: 17587173 INFO @ Tue, 16 Jun 2020 09:13:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:38: #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 09:13:38: #1 tags after filtering in treatment: 17587173 INFO @ Tue, 16 Jun 2020 09:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:39: #2 number of paired peaks: 213 WARNING @ Tue, 16 Jun 2020 09:13:39: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:39: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:13:39: #2 alternative fragment length(s) may be 1,37,541,576 bps INFO @ Tue, 16 Jun 2020 09:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.10_model.r WARNING @ Tue, 16 Jun 2020 09:13:39: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:39: #2 You may need to consider one of the other alternative d(s): 1,37,541,576 WARNING @ Tue, 16 Jun 2020 09:13:39: #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 09:13:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:41: 12000000 INFO @ Tue, 16 Jun 2020 09:13:46: 13000000 INFO @ Tue, 16 Jun 2020 09:13:50: 14000000 INFO @ Tue, 16 Jun 2020 09:13:55: 15000000 INFO @ Tue, 16 Jun 2020 09:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.05_summits.bed INFO @ Tue, 16 Jun 2020 09:13:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (679 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:00: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:14:04: 17000000 INFO @ Tue, 16 Jun 2020 09:14:07: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:07: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:07: #1 total tags in treatment: 17587173 INFO @ Tue, 16 Jun 2020 09:14:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:07: #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 09:14:07: #1 tags after filtering in treatment: 17587173 INFO @ Tue, 16 Jun 2020 09:14:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:09: #2 number of paired peaks: 213 WARNING @ Tue, 16 Jun 2020 09:14:09: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:09: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:14:09: #2 alternative fragment length(s) may be 1,37,541,576 bps INFO @ Tue, 16 Jun 2020 09:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.20_model.r WARNING @ Tue, 16 Jun 2020 09:14:09: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:14:09: #2 You may need to consider one of the other alternative d(s): 1,37,541,576 WARNING @ Tue, 16 Jun 2020 09:14:09: #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 09:14:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.10_summits.bed INFO @ Tue, 16 Jun 2020 09:14:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (330 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:14:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466503/SRX466503.20_summits.bed INFO @ Tue, 16 Jun 2020 09:14:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (99 records, 4 fields): 1 millis CompletedMACS2peakCalling