Job ID = 6368176 SRX = SRX494860 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:05 prefetch.2.10.7: 1) Downloading 'SRR1198392'... 2020-06-16T00:14:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:16:19 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:16:19 prefetch.2.10.7: 1) 'SRR1198392' was downloaded successfully Read 18388946 spots for SRR1198392/SRR1198392.sra Written 18388946 spots for SRR1198392/SRR1198392.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: 00:03:52 18388946 reads; of these: 18388946 (100.00%) were unpaired; of these: 4337223 (23.59%) aligned 0 times 11668017 (63.45%) aligned exactly 1 time 2383706 (12.96%) aligned >1 times 76.41% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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 8 files... [bam_rmdupse_core] 1117661 / 14051723 = 0.0795 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 09:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.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 09:25:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:13: 1000000 INFO @ Tue, 16 Jun 2020 09:25:19: 2000000 INFO @ Tue, 16 Jun 2020 09:25:25: 3000000 INFO @ Tue, 16 Jun 2020 09:25:30: 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 09:25:36: 5000000 INFO @ Tue, 16 Jun 2020 09:25:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.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 09:25:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:42: 6000000 INFO @ Tue, 16 Jun 2020 09:25:43: 1000000 INFO @ Tue, 16 Jun 2020 09:25:47: 7000000 INFO @ Tue, 16 Jun 2020 09:25:49: 2000000 INFO @ Tue, 16 Jun 2020 09:25:53: 8000000 INFO @ Tue, 16 Jun 2020 09:25:55: 3000000 INFO @ Tue, 16 Jun 2020 09:25:59: 9000000 INFO @ Tue, 16 Jun 2020 09:26:01: 4000000 INFO @ Tue, 16 Jun 2020 09:26:04: 10000000 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 09:26:06: 5000000 INFO @ Tue, 16 Jun 2020 09:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.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 09:26:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:10: 11000000 INFO @ Tue, 16 Jun 2020 09:26:12: 6000000 INFO @ Tue, 16 Jun 2020 09:26:13: 1000000 INFO @ Tue, 16 Jun 2020 09:26:16: 12000000 INFO @ Tue, 16 Jun 2020 09:26:18: 7000000 INFO @ Tue, 16 Jun 2020 09:26:19: 2000000 INFO @ Tue, 16 Jun 2020 09:26:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:26:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:26:21: #1 total tags in treatment: 12934062 INFO @ Tue, 16 Jun 2020 09:26:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:21: #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 09:26:21: #1 tags after filtering in treatment: 12934062 INFO @ Tue, 16 Jun 2020 09:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:22: #2 number of paired peaks: 334 WARNING @ Tue, 16 Jun 2020 09:26:22: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:22: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:26:22: #2 alternative fragment length(s) may be 2,42,556,564,586 bps INFO @ Tue, 16 Jun 2020 09:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.05_model.r WARNING @ Tue, 16 Jun 2020 09:26:22: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:22: #2 You may need to consider one of the other alternative d(s): 2,42,556,564,586 WARNING @ Tue, 16 Jun 2020 09:26:22: #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 09:26:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:24: 8000000 INFO @ Tue, 16 Jun 2020 09:26:24: 3000000 INFO @ Tue, 16 Jun 2020 09:26:29: 9000000 INFO @ Tue, 16 Jun 2020 09:26:30: 4000000 INFO @ Tue, 16 Jun 2020 09:26:35: 10000000 INFO @ Tue, 16 Jun 2020 09:26:36: 5000000 INFO @ Tue, 16 Jun 2020 09:26:40: 11000000 INFO @ Tue, 16 Jun 2020 09:26:41: 6000000 INFO @ Tue, 16 Jun 2020 09:26:46: 12000000 INFO @ Tue, 16 Jun 2020 09:26:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:47: 7000000 INFO @ Tue, 16 Jun 2020 09:26:51: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:26:51: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:26:51: #1 total tags in treatment: 12934062 INFO @ Tue, 16 Jun 2020 09:26:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:51: #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 09:26:52: #1 tags after filtering in treatment: 12934062 INFO @ Tue, 16 Jun 2020 09:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:52: #2 number of paired peaks: 334 WARNING @ Tue, 16 Jun 2020 09:26:52: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:53: 8000000 INFO @ Tue, 16 Jun 2020 09:26:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:53: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:26:53: #2 alternative fragment length(s) may be 2,42,556,564,586 bps INFO @ Tue, 16 Jun 2020 09:26:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:53: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:53: #2 You may need to consider one of the other alternative d(s): 2,42,556,564,586 WARNING @ Tue, 16 Jun 2020 09:26:53: #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 09:26:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:58: 9000000 INFO @ Tue, 16 Jun 2020 09:26:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (695 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:03: 10000000 INFO @ Tue, 16 Jun 2020 09:27:08: 11000000 INFO @ Tue, 16 Jun 2020 09:27:14: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:27:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:27:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:27:19: #1 total tags in treatment: 12934062 INFO @ Tue, 16 Jun 2020 09:27:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:19: #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 09:27:19: #1 tags after filtering in treatment: 12934062 INFO @ Tue, 16 Jun 2020 09:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:20: #2 number of paired peaks: 334 WARNING @ Tue, 16 Jun 2020 09:27:20: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:20: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:27:20: #2 alternative fragment length(s) may be 2,42,556,564,586 bps INFO @ Tue, 16 Jun 2020 09:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.20_model.r WARNING @ Tue, 16 Jun 2020 09:27:20: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:20: #2 You may need to consider one of the other alternative d(s): 2,42,556,564,586 WARNING @ Tue, 16 Jun 2020 09:27:20: #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 09:27:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (457 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494860/SRX494860.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 1 millis CompletedMACS2peakCalling