Job ID = 6367898 SRX = SRX4194188 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:38:02 prefetch.2.10.7: 1) Downloading 'SRR7291450'... 2020-06-15T23:38:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:39:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:39:11 prefetch.2.10.7: 'SRR7291450' is valid 2020-06-15T23:39:11 prefetch.2.10.7: 1) 'SRR7291450' was downloaded successfully 2020-06-15T23:39:11 prefetch.2.10.7: 'SRR7291450' has 0 unresolved dependencies Read 4888993 spots for SRR7291450/SRR7291450.sra Written 4888993 spots for SRR7291450/SRR7291450.sra 2020-06-15T23:39:43 prefetch.2.10.7: 1) Downloading 'SRR7291451'... 2020-06-15T23:39:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:45 prefetch.2.10.7: 'SRR7291451' is valid 2020-06-15T23:40:45 prefetch.2.10.7: 1) 'SRR7291451' was downloaded successfully 2020-06-15T23:40:45 prefetch.2.10.7: 'SRR7291451' has 0 unresolved dependencies Read 4764869 spots for SRR7291451/SRR7291451.sra Written 4764869 spots for SRR7291451/SRR7291451.sra 2020-06-15T23:41:17 prefetch.2.10.7: 1) Downloading 'SRR7291452'... 2020-06-15T23:41:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:19 prefetch.2.10.7: 'SRR7291452' is valid 2020-06-15T23:42:19 prefetch.2.10.7: 1) 'SRR7291452' was downloaded successfully 2020-06-15T23:42:20 prefetch.2.10.7: 'SRR7291452' has 0 unresolved dependencies Read 4871183 spots for SRR7291452/SRR7291452.sra Written 4871183 spots for SRR7291452/SRR7291452.sra 2020-06-15T23:42:51 prefetch.2.10.7: 1) Downloading 'SRR7291453'... 2020-06-15T23:42:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:14 prefetch.2.10.7: 'SRR7291453' is valid 2020-06-15T23:44:14 prefetch.2.10.7: 1) 'SRR7291453' was downloaded successfully 2020-06-15T23:44:14 prefetch.2.10.7: 'SRR7291453' has 0 unresolved dependencies Read 4726826 spots for SRR7291453/SRR7291453.sra Written 4726826 spots for SRR7291453/SRR7291453.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: 00:07:36 19251871 reads; of these: 19251871 (100.00%) were unpaired; of these: 449135 (2.33%) aligned 0 times 13948657 (72.45%) aligned exactly 1 time 4854079 (25.21%) aligned >1 times 97.67% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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 8 files... [bam_rmdupse_core] 6291873 / 18802736 = 0.3346 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 08:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.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 08:58:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:18: 1000000 INFO @ Tue, 16 Jun 2020 08:58:26: 2000000 INFO @ Tue, 16 Jun 2020 08:58:33: 3000000 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 08:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.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 08:58:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:41: 4000000 INFO @ Tue, 16 Jun 2020 08:58:48: 1000000 INFO @ Tue, 16 Jun 2020 08:58:49: 5000000 INFO @ Tue, 16 Jun 2020 08:58:55: 2000000 INFO @ Tue, 16 Jun 2020 08:58:58: 6000000 INFO @ Tue, 16 Jun 2020 08:59:02: 3000000 INFO @ Tue, 16 Jun 2020 08:59:06: 7000000 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 08:59:10: 4000000 INFO @ Tue, 16 Jun 2020 08:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.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 08:59:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:14: 8000000 INFO @ Tue, 16 Jun 2020 08:59:17: 5000000 INFO @ Tue, 16 Jun 2020 08:59:19: 1000000 INFO @ Tue, 16 Jun 2020 08:59:22: 9000000 INFO @ Tue, 16 Jun 2020 08:59:25: 6000000 INFO @ Tue, 16 Jun 2020 08:59:27: 2000000 INFO @ Tue, 16 Jun 2020 08:59:30: 10000000 INFO @ Tue, 16 Jun 2020 08:59:33: 7000000 INFO @ Tue, 16 Jun 2020 08:59:36: 3000000 INFO @ Tue, 16 Jun 2020 08:59:39: 11000000 INFO @ Tue, 16 Jun 2020 08:59:40: 8000000 INFO @ Tue, 16 Jun 2020 08:59:44: 4000000 INFO @ Tue, 16 Jun 2020 08:59:47: 12000000 INFO @ Tue, 16 Jun 2020 08:59:48: 9000000 INFO @ Tue, 16 Jun 2020 08:59:52: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:59:52: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:59:52: #1 total tags in treatment: 12510863 INFO @ Tue, 16 Jun 2020 08:59:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:52: #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 08:59:52: #1 tags after filtering in treatment: 12510863 INFO @ Tue, 16 Jun 2020 08:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:53: 5000000 INFO @ Tue, 16 Jun 2020 08:59:53: #2 number of paired peaks: 604 WARNING @ Tue, 16 Jun 2020 08:59:53: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:53: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 08:59:53: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 16 Jun 2020 08:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.05_model.r WARNING @ Tue, 16 Jun 2020 08:59:53: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:53: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 16 Jun 2020 08:59:53: #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 08:59:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:56: 10000000 INFO @ Tue, 16 Jun 2020 09:00:01: 6000000 INFO @ Tue, 16 Jun 2020 09:00:03: 11000000 INFO @ Tue, 16 Jun 2020 09:00:09: 7000000 INFO @ Tue, 16 Jun 2020 09:00:11: 12000000 INFO @ Tue, 16 Jun 2020 09:00:15: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:00:15: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:00:15: #1 total tags in treatment: 12510863 INFO @ Tue, 16 Jun 2020 09:00:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:15: #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 09:00:15: #1 tags after filtering in treatment: 12510863 INFO @ Tue, 16 Jun 2020 09:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:16: #2 number of paired peaks: 604 WARNING @ Tue, 16 Jun 2020 09:00:16: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:16: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 09:00:16: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 16 Jun 2020 09:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.10_model.r WARNING @ Tue, 16 Jun 2020 09:00:16: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:16: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 16 Jun 2020 09:00:16: #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 09:00:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:00:18: 8000000 INFO @ Tue, 16 Jun 2020 09:00:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:26: 9000000 INFO @ Tue, 16 Jun 2020 09:00:34: 10000000 INFO @ Tue, 16 Jun 2020 09:00:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.05_summits.bed INFO @ Tue, 16 Jun 2020 09:00:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1793 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:43: 11000000 INFO @ Tue, 16 Jun 2020 09:00:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:00:51: 12000000 INFO @ Tue, 16 Jun 2020 09:00:56: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:00:56: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:00:56: #1 total tags in treatment: 12510863 INFO @ Tue, 16 Jun 2020 09:00:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:56: #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 09:00:56: #1 tags after filtering in treatment: 12510863 INFO @ Tue, 16 Jun 2020 09:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:57: #2 number of paired peaks: 604 WARNING @ Tue, 16 Jun 2020 09:00:57: Fewer paired peaks (604) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 604 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:57: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 09:00:57: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 16 Jun 2020 09:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.20_model.r WARNING @ Tue, 16 Jun 2020 09:00:57: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:57: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 16 Jun 2020 09:00:57: #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 09:00:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (766 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:01:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194188/SRX4194188.20_summits.bed INFO @ Tue, 16 Jun 2020 09:01:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (298 records, 4 fields): 2 millis CompletedMACS2peakCalling