Job ID = 6367911 SRX = SRX4194204 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:03 prefetch.2.10.7: 1) Downloading 'SRR7291504'... 2020-06-15T23:47:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:08 prefetch.2.10.7: 'SRR7291504' is valid 2020-06-15T23:48:08 prefetch.2.10.7: 1) 'SRR7291504' was downloaded successfully 2020-06-15T23:48:08 prefetch.2.10.7: 'SRR7291504' has 0 unresolved dependencies Read 5699445 spots for SRR7291504/SRR7291504.sra Written 5699445 spots for SRR7291504/SRR7291504.sra 2020-06-15T23:48:52 prefetch.2.10.7: 1) Downloading 'SRR7291505'... 2020-06-15T23:48:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:50 prefetch.2.10.7: 'SRR7291505' is valid 2020-06-15T23:49:50 prefetch.2.10.7: 1) 'SRR7291505' was downloaded successfully 2020-06-15T23:49:50 prefetch.2.10.7: 'SRR7291505' has 0 unresolved dependencies Read 5559787 spots for SRR7291505/SRR7291505.sra Written 5559787 spots for SRR7291505/SRR7291505.sra 2020-06-15T23:50:26 prefetch.2.10.7: 1) Downloading 'SRR7291506'... 2020-06-15T23:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:13 prefetch.2.10.7: 'SRR7291506' is valid 2020-06-15T23:51:13 prefetch.2.10.7: 1) 'SRR7291506' was downloaded successfully 2020-06-15T23:51:13 prefetch.2.10.7: 'SRR7291506' has 0 unresolved dependencies Read 5697305 spots for SRR7291506/SRR7291506.sra Written 5697305 spots for SRR7291506/SRR7291506.sra 2020-06-15T23:51:44 prefetch.2.10.7: 1) Downloading 'SRR7291507'... 2020-06-15T23:51:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:40 prefetch.2.10.7: 'SRR7291507' is valid 2020-06-15T23:52:40 prefetch.2.10.7: 1) 'SRR7291507' was downloaded successfully 2020-06-15T23:52:40 prefetch.2.10.7: 'SRR7291507' has 0 unresolved dependencies Read 5501410 spots for SRR7291507/SRR7291507.sra Written 5501410 spots for SRR7291507/SRR7291507.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: 00:08:36 22457947 reads; of these: 22457947 (100.00%) were unpaired; of these: 710533 (3.16%) aligned 0 times 18603709 (82.84%) aligned exactly 1 time 3143705 (14.00%) aligned >1 times 96.84% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 3506449 / 21747414 = 0.1612 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 09:09:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.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 09:09:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:14: 1000000 INFO @ Tue, 16 Jun 2020 09:09:20: 2000000 INFO @ Tue, 16 Jun 2020 09:09:27: 3000000 INFO @ Tue, 16 Jun 2020 09:09:34: 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 09:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.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 09:09:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:41: 5000000 INFO @ Tue, 16 Jun 2020 09:09:45: 1000000 INFO @ Tue, 16 Jun 2020 09:09:48: 6000000 INFO @ Tue, 16 Jun 2020 09:09:53: 2000000 INFO @ Tue, 16 Jun 2020 09:09:56: 7000000 INFO @ Tue, 16 Jun 2020 09:10:01: 3000000 INFO @ Tue, 16 Jun 2020 09:10:03: 8000000 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 09:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.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 09:10:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:09: 4000000 INFO @ Tue, 16 Jun 2020 09:10:11: 9000000 INFO @ Tue, 16 Jun 2020 09:10:15: 1000000 INFO @ Tue, 16 Jun 2020 09:10:17: 5000000 INFO @ Tue, 16 Jun 2020 09:10:19: 10000000 INFO @ Tue, 16 Jun 2020 09:10:23: 2000000 INFO @ Tue, 16 Jun 2020 09:10:25: 6000000 INFO @ Tue, 16 Jun 2020 09:10:26: 11000000 INFO @ Tue, 16 Jun 2020 09:10:31: 3000000 INFO @ Tue, 16 Jun 2020 09:10:33: 7000000 INFO @ Tue, 16 Jun 2020 09:10:34: 12000000 INFO @ Tue, 16 Jun 2020 09:10:38: 4000000 INFO @ Tue, 16 Jun 2020 09:10:40: 8000000 INFO @ Tue, 16 Jun 2020 09:10:42: 13000000 INFO @ Tue, 16 Jun 2020 09:10:46: 5000000 INFO @ Tue, 16 Jun 2020 09:10:48: 9000000 INFO @ Tue, 16 Jun 2020 09:10:50: 14000000 INFO @ Tue, 16 Jun 2020 09:10:54: 6000000 INFO @ Tue, 16 Jun 2020 09:10:56: 10000000 INFO @ Tue, 16 Jun 2020 09:10:57: 15000000 INFO @ Tue, 16 Jun 2020 09:11:01: 7000000 INFO @ Tue, 16 Jun 2020 09:11:04: 11000000 INFO @ Tue, 16 Jun 2020 09:11:05: 16000000 INFO @ Tue, 16 Jun 2020 09:11:09: 8000000 INFO @ Tue, 16 Jun 2020 09:11:12: 12000000 INFO @ Tue, 16 Jun 2020 09:11:13: 17000000 INFO @ Tue, 16 Jun 2020 09:11:17: 9000000 INFO @ Tue, 16 Jun 2020 09:11:21: 13000000 INFO @ Tue, 16 Jun 2020 09:11:21: 18000000 INFO @ Tue, 16 Jun 2020 09:11:23: #1 tag size is determined as 70 bps INFO @ Tue, 16 Jun 2020 09:11:23: #1 tag size = 70 INFO @ Tue, 16 Jun 2020 09:11:23: #1 total tags in treatment: 18240965 INFO @ Tue, 16 Jun 2020 09:11:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:23: #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 09:11:23: #1 tags after filtering in treatment: 18240965 INFO @ Tue, 16 Jun 2020 09:11:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:25: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 09:11:25: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:25: 10000000 INFO @ Tue, 16 Jun 2020 09:11:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:25: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:11:25: #2 alternative fragment length(s) may be 2,66,540,570 bps INFO @ Tue, 16 Jun 2020 09:11:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:25: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:25: #2 You may need to consider one of the other alternative d(s): 2,66,540,570 WARNING @ Tue, 16 Jun 2020 09:11:25: #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 09:11:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:28: 14000000 INFO @ Tue, 16 Jun 2020 09:11:32: 11000000 INFO @ Tue, 16 Jun 2020 09:11:36: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:40: 12000000 INFO @ Tue, 16 Jun 2020 09:11:44: 16000000 INFO @ Tue, 16 Jun 2020 09:11:48: 13000000 INFO @ Tue, 16 Jun 2020 09:11:52: 17000000 INFO @ Tue, 16 Jun 2020 09:11:56: 14000000 INFO @ Tue, 16 Jun 2020 09:12:00: 18000000 INFO @ Tue, 16 Jun 2020 09:12:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:02: #1 tag size is determined as 70 bps INFO @ Tue, 16 Jun 2020 09:12:02: #1 tag size = 70 INFO @ Tue, 16 Jun 2020 09:12:02: #1 total tags in treatment: 18240965 INFO @ Tue, 16 Jun 2020 09:12:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:02: #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 09:12:03: #1 tags after filtering in treatment: 18240965 INFO @ Tue, 16 Jun 2020 09:12:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:04: 15000000 INFO @ Tue, 16 Jun 2020 09:12:04: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 09:12:04: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:04: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:12:04: #2 alternative fragment length(s) may be 2,66,540,570 bps INFO @ Tue, 16 Jun 2020 09:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:04: #2 You may need to consider one of the other alternative d(s): 2,66,540,570 WARNING @ Tue, 16 Jun 2020 09:12:04: #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 09:12:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:11: 16000000 INFO @ Tue, 16 Jun 2020 09:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1468 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:18: 17000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:25: 18000000 INFO @ Tue, 16 Jun 2020 09:12:27: #1 tag size is determined as 70 bps INFO @ Tue, 16 Jun 2020 09:12:27: #1 tag size = 70 INFO @ Tue, 16 Jun 2020 09:12:27: #1 total tags in treatment: 18240965 INFO @ Tue, 16 Jun 2020 09:12:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:27: #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 09:12:27: #1 tags after filtering in treatment: 18240965 INFO @ Tue, 16 Jun 2020 09:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:29: #2 number of paired peaks: 149 WARNING @ Tue, 16 Jun 2020 09:12:29: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:29: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:12:29: #2 alternative fragment length(s) may be 2,66,540,570 bps INFO @ Tue, 16 Jun 2020 09:12:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:29: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:29: #2 You may need to consider one of the other alternative d(s): 2,66,540,570 WARNING @ Tue, 16 Jun 2020 09:12:29: #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 09:12:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194204/SRX4194204.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling