Job ID = 6368311 SRX = SRX494994 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:07:24 prefetch.2.10.7: 1) Downloading 'SRR1198526'... 2020-06-16T00:07:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:12:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:12:53 prefetch.2.10.7: 1) 'SRR1198526' was downloaded successfully Read 22621140 spots for SRR1198526/SRR1198526.sra Written 22621140 spots for SRR1198526/SRR1198526.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: 00:04:15 22621140 reads; of these: 22621140 (100.00%) were unpaired; of these: 260930 (1.15%) aligned 0 times 18792521 (83.08%) aligned exactly 1 time 3567689 (15.77%) aligned >1 times 98.85% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 3355469 / 22360210 = 0.1501 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 09:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.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 09:23:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:04: 1000000 INFO @ Tue, 16 Jun 2020 09:24:09: 2000000 INFO @ Tue, 16 Jun 2020 09:24:14: 3000000 INFO @ Tue, 16 Jun 2020 09:24:19: 4000000 INFO @ Tue, 16 Jun 2020 09:24:24: 5000000 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 09:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.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 09:24:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:29: 6000000 INFO @ Tue, 16 Jun 2020 09:24:34: 7000000 INFO @ Tue, 16 Jun 2020 09:24:35: 1000000 INFO @ Tue, 16 Jun 2020 09:24:39: 8000000 INFO @ Tue, 16 Jun 2020 09:24:40: 2000000 INFO @ Tue, 16 Jun 2020 09:24:44: 9000000 INFO @ Tue, 16 Jun 2020 09:24:45: 3000000 INFO @ Tue, 16 Jun 2020 09:24:49: 10000000 INFO @ Tue, 16 Jun 2020 09:24:51: 4000000 INFO @ Tue, 16 Jun 2020 09:24:54: 11000000 INFO @ Tue, 16 Jun 2020 09:24:56: 5000000 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 09:24:59: 12000000 INFO @ Tue, 16 Jun 2020 09:24:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.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 09:24:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:02: 6000000 INFO @ Tue, 16 Jun 2020 09:25:04: 13000000 INFO @ Tue, 16 Jun 2020 09:25:04: 1000000 INFO @ Tue, 16 Jun 2020 09:25:07: 7000000 INFO @ Tue, 16 Jun 2020 09:25:09: 14000000 INFO @ Tue, 16 Jun 2020 09:25:09: 2000000 INFO @ Tue, 16 Jun 2020 09:25:13: 8000000 INFO @ Tue, 16 Jun 2020 09:25:14: 15000000 INFO @ Tue, 16 Jun 2020 09:25:14: 3000000 INFO @ Tue, 16 Jun 2020 09:25:18: 9000000 INFO @ Tue, 16 Jun 2020 09:25:19: 16000000 INFO @ Tue, 16 Jun 2020 09:25:19: 4000000 INFO @ Tue, 16 Jun 2020 09:25:24: 17000000 INFO @ Tue, 16 Jun 2020 09:25:24: 10000000 INFO @ Tue, 16 Jun 2020 09:25:25: 5000000 INFO @ Tue, 16 Jun 2020 09:25:29: 18000000 INFO @ Tue, 16 Jun 2020 09:25:30: 6000000 INFO @ Tue, 16 Jun 2020 09:25:30: 11000000 INFO @ Tue, 16 Jun 2020 09:25:34: 19000000 INFO @ Tue, 16 Jun 2020 09:25:34: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:25:34: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:25:34: #1 total tags in treatment: 19004741 INFO @ Tue, 16 Jun 2020 09:25:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:34: #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 09:25:34: #1 tags after filtering in treatment: 19004741 INFO @ Tue, 16 Jun 2020 09:25:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:35: 7000000 INFO @ Tue, 16 Jun 2020 09:25:35: 12000000 INFO @ Tue, 16 Jun 2020 09:25:36: #2 number of paired peaks: 226 WARNING @ Tue, 16 Jun 2020 09:25:36: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:36: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:25:36: #2 alternative fragment length(s) may be 1,39,580 bps INFO @ Tue, 16 Jun 2020 09:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.05_model.r WARNING @ Tue, 16 Jun 2020 09:25:36: #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 09:25:36: #2 You may need to consider one of the other alternative d(s): 1,39,580 WARNING @ Tue, 16 Jun 2020 09:25:36: #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 09:25:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:39: 8000000 INFO @ Tue, 16 Jun 2020 09:25:41: 13000000 INFO @ Tue, 16 Jun 2020 09:25:44: 9000000 INFO @ Tue, 16 Jun 2020 09:25:46: 14000000 INFO @ Tue, 16 Jun 2020 09:25:49: 10000000 INFO @ Tue, 16 Jun 2020 09:25:52: 15000000 INFO @ Tue, 16 Jun 2020 09:25:54: 11000000 INFO @ Tue, 16 Jun 2020 09:25:58: 16000000 INFO @ Tue, 16 Jun 2020 09:25:59: 12000000 INFO @ Tue, 16 Jun 2020 09:26:04: 17000000 INFO @ Tue, 16 Jun 2020 09:26:04: 13000000 INFO @ Tue, 16 Jun 2020 09:26:09: 14000000 INFO @ Tue, 16 Jun 2020 09:26:09: 18000000 INFO @ Tue, 16 Jun 2020 09:26:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:14: 15000000 INFO @ Tue, 16 Jun 2020 09:26:15: 19000000 INFO @ Tue, 16 Jun 2020 09:26:15: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:15: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:15: #1 total tags in treatment: 19004741 INFO @ Tue, 16 Jun 2020 09:26:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:15: #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 09:26:15: #1 tags after filtering in treatment: 19004741 INFO @ Tue, 16 Jun 2020 09:26:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:17: #2 number of paired peaks: 226 WARNING @ Tue, 16 Jun 2020 09:26:17: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:17: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:26:17: #2 alternative fragment length(s) may be 1,39,580 bps INFO @ Tue, 16 Jun 2020 09:26:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:17: #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 09:26:17: #2 You may need to consider one of the other alternative d(s): 1,39,580 WARNING @ Tue, 16 Jun 2020 09:26:17: #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 09:26:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:19: 16000000 INFO @ Tue, 16 Jun 2020 09:26:24: 17000000 INFO @ Tue, 16 Jun 2020 09:26:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (724 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:29: 18000000 INFO @ Tue, 16 Jun 2020 09:26:34: 19000000 INFO @ Tue, 16 Jun 2020 09:26:34: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:26:34: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:26:34: #1 total tags in treatment: 19004741 INFO @ Tue, 16 Jun 2020 09:26:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:34: #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 09:26:34: #1 tags after filtering in treatment: 19004741 INFO @ Tue, 16 Jun 2020 09:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:36: #2 number of paired peaks: 226 WARNING @ Tue, 16 Jun 2020 09:26:36: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:36: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 09:26:36: #2 alternative fragment length(s) may be 1,39,580 bps INFO @ Tue, 16 Jun 2020 09:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.20_model.r WARNING @ Tue, 16 Jun 2020 09:26:36: #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 09:26:36: #2 You may need to consider one of the other alternative d(s): 1,39,580 WARNING @ Tue, 16 Jun 2020 09:26:36: #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 09:26:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:36: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494994/SRX494994.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。