Job ID = 6367916 SRX = SRX4194210 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:59 prefetch.2.10.7: 1) Downloading 'SRR7291525'... 2020-06-15T23:47:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:28 prefetch.2.10.7: 'SRR7291525' is valid 2020-06-15T23:49:28 prefetch.2.10.7: 1) 'SRR7291525' was downloaded successfully 2020-06-15T23:49:28 prefetch.2.10.7: 'SRR7291525' has 0 unresolved dependencies Read 6534095 spots for SRR7291525/SRR7291525.sra Written 6534095 spots for SRR7291525/SRR7291525.sra 2020-06-15T23:50:03 prefetch.2.10.7: 1) Downloading 'SRR7291527'... 2020-06-15T23:50:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:58 prefetch.2.10.7: 'SRR7291527' is valid 2020-06-15T23:50:58 prefetch.2.10.7: 1) 'SRR7291527' was downloaded successfully 2020-06-15T23:50:58 prefetch.2.10.7: 'SRR7291527' has 0 unresolved dependencies Read 6386147 spots for SRR7291527/SRR7291527.sra Written 6386147 spots for SRR7291527/SRR7291527.sra 2020-06-15T23:51:33 prefetch.2.10.7: 1) Downloading 'SRR7291528'... 2020-06-15T23:51:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:34 prefetch.2.10.7: 'SRR7291528' is valid 2020-06-15T23:52:34 prefetch.2.10.7: 1) 'SRR7291528' was downloaded successfully 2020-06-15T23:52:34 prefetch.2.10.7: 'SRR7291528' has 0 unresolved dependencies Read 6524006 spots for SRR7291528/SRR7291528.sra Written 6524006 spots for SRR7291528/SRR7291528.sra 2020-06-15T23:53:09 prefetch.2.10.7: 1) Downloading 'SRR7291529'... 2020-06-15T23:53:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:02 prefetch.2.10.7: 'SRR7291529' is valid 2020-06-15T23:54:02 prefetch.2.10.7: 1) 'SRR7291529' was downloaded successfully 2020-06-15T23:54:02 prefetch.2.10.7: 'SRR7291529' has 0 unresolved dependencies Read 6315285 spots for SRR7291529/SRR7291529.sra Written 6315285 spots for SRR7291529/SRR7291529.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: 00:09:52 25759533 reads; of these: 25759533 (100.00%) were unpaired; of these: 334096 (1.30%) aligned 0 times 21480173 (83.39%) aligned exactly 1 time 3945264 (15.32%) aligned >1 times 98.70% overall alignment rate Time searching: 00:09:52 Overall time: 00:09:52 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] 4025785 / 25425437 = 0.1583 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 09:12:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.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 09:12:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:57: 1000000 INFO @ Tue, 16 Jun 2020 09:13:03: 2000000 INFO @ Tue, 16 Jun 2020 09:13:09: 3000000 INFO @ Tue, 16 Jun 2020 09:13:15: 4000000 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 09:13:21: 5000000 INFO @ Tue, 16 Jun 2020 09:13:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.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 09:13:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:28: 6000000 INFO @ Tue, 16 Jun 2020 09:13:28: 1000000 INFO @ Tue, 16 Jun 2020 09:13:34: 2000000 INFO @ Tue, 16 Jun 2020 09:13:34: 7000000 INFO @ Tue, 16 Jun 2020 09:13:40: 8000000 INFO @ Tue, 16 Jun 2020 09:13:40: 3000000 INFO @ Tue, 16 Jun 2020 09:13:47: 9000000 INFO @ Tue, 16 Jun 2020 09:13:47: 4000000 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 09:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.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 09:13:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:53: 10000000 INFO @ Tue, 16 Jun 2020 09:13:53: 5000000 INFO @ Tue, 16 Jun 2020 09:13:58: 1000000 INFO @ Tue, 16 Jun 2020 09:13:59: 11000000 INFO @ Tue, 16 Jun 2020 09:14:00: 6000000 INFO @ Tue, 16 Jun 2020 09:14:04: 2000000 INFO @ Tue, 16 Jun 2020 09:14:06: 12000000 INFO @ Tue, 16 Jun 2020 09:14:06: 7000000 INFO @ Tue, 16 Jun 2020 09:14:11: 3000000 INFO @ Tue, 16 Jun 2020 09:14:12: 13000000 INFO @ Tue, 16 Jun 2020 09:14:12: 8000000 INFO @ Tue, 16 Jun 2020 09:14:17: 4000000 INFO @ Tue, 16 Jun 2020 09:14:18: 14000000 INFO @ Tue, 16 Jun 2020 09:14:19: 9000000 INFO @ Tue, 16 Jun 2020 09:14:23: 5000000 INFO @ Tue, 16 Jun 2020 09:14:25: 15000000 INFO @ Tue, 16 Jun 2020 09:14:25: 10000000 INFO @ Tue, 16 Jun 2020 09:14:30: 6000000 INFO @ Tue, 16 Jun 2020 09:14:31: 16000000 INFO @ Tue, 16 Jun 2020 09:14:32: 11000000 INFO @ Tue, 16 Jun 2020 09:14:36: 7000000 INFO @ Tue, 16 Jun 2020 09:14:37: 17000000 INFO @ Tue, 16 Jun 2020 09:14:38: 12000000 INFO @ Tue, 16 Jun 2020 09:14:42: 8000000 INFO @ Tue, 16 Jun 2020 09:14:43: 18000000 INFO @ Tue, 16 Jun 2020 09:14:44: 13000000 INFO @ Tue, 16 Jun 2020 09:14:49: 9000000 INFO @ Tue, 16 Jun 2020 09:14:50: 19000000 INFO @ Tue, 16 Jun 2020 09:14:50: 14000000 INFO @ Tue, 16 Jun 2020 09:14:55: 10000000 INFO @ Tue, 16 Jun 2020 09:14:56: 20000000 INFO @ Tue, 16 Jun 2020 09:14:57: 15000000 INFO @ Tue, 16 Jun 2020 09:15:01: 11000000 INFO @ Tue, 16 Jun 2020 09:15:02: 21000000 INFO @ Tue, 16 Jun 2020 09:15:03: 16000000 INFO @ Tue, 16 Jun 2020 09:15:05: #1 tag size is determined as 72 bps INFO @ Tue, 16 Jun 2020 09:15:05: #1 tag size = 72 INFO @ Tue, 16 Jun 2020 09:15:05: #1 total tags in treatment: 21399652 INFO @ Tue, 16 Jun 2020 09:15:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:05: #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 09:15:05: #1 tags after filtering in treatment: 21399652 INFO @ Tue, 16 Jun 2020 09:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:07: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:15:07: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:07: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:15:07: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 16 Jun 2020 09:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.05_model.r WARNING @ Tue, 16 Jun 2020 09:15:07: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:15:07: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 16 Jun 2020 09:15:07: #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 09:15:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:07: 12000000 INFO @ Tue, 16 Jun 2020 09:15:09: 17000000 INFO @ Tue, 16 Jun 2020 09:15:13: 13000000 INFO @ Tue, 16 Jun 2020 09:15:16: 18000000 INFO @ Tue, 16 Jun 2020 09:15:19: 14000000 INFO @ Tue, 16 Jun 2020 09:15:22: 19000000 INFO @ Tue, 16 Jun 2020 09:15:26: 15000000 INFO @ Tue, 16 Jun 2020 09:15:28: 20000000 INFO @ Tue, 16 Jun 2020 09:15:32: 16000000 INFO @ Tue, 16 Jun 2020 09:15:34: 21000000 INFO @ Tue, 16 Jun 2020 09:15:37: #1 tag size is determined as 72 bps INFO @ Tue, 16 Jun 2020 09:15:37: #1 tag size = 72 INFO @ Tue, 16 Jun 2020 09:15:37: #1 total tags in treatment: 21399652 INFO @ Tue, 16 Jun 2020 09:15:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:37: #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 09:15:37: #1 tags after filtering in treatment: 21399652 INFO @ Tue, 16 Jun 2020 09:15:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:38: 17000000 INFO @ Tue, 16 Jun 2020 09:15:38: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:15:38: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:39: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:15:39: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 16 Jun 2020 09:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.10_model.r WARNING @ Tue, 16 Jun 2020 09:15:39: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:15:39: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 16 Jun 2020 09:15:39: #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 09:15:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:44: 18000000 INFO @ Tue, 16 Jun 2020 09:15:50: 19000000 INFO @ Tue, 16 Jun 2020 09:15:56: 20000000 INFO @ Tue, 16 Jun 2020 09:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (667 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:01: 21000000 INFO @ Tue, 16 Jun 2020 09:16:04: #1 tag size is determined as 72 bps INFO @ Tue, 16 Jun 2020 09:16:04: #1 tag size = 72 INFO @ Tue, 16 Jun 2020 09:16:04: #1 total tags in treatment: 21399652 INFO @ Tue, 16 Jun 2020 09:16:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:04: #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 09:16:04: #1 tags after filtering in treatment: 21399652 INFO @ Tue, 16 Jun 2020 09:16:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:06: #2 number of paired peaks: 174 WARNING @ Tue, 16 Jun 2020 09:16:06: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:06: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:16:06: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 16 Jun 2020 09:16:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.20_model.r WARNING @ Tue, 16 Jun 2020 09:16:06: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:06: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 16 Jun 2020 09:16:06: #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 09:16:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.10_summits.bed INFO @ Tue, 16 Jun 2020 09:16:32: Done! BigWig に変換しました。 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194210/SRX4194210.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 1 millis CompletedMACS2peakCalling