Job ID = 6366564 SRX = SRX1936242 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:56:14 prefetch.2.10.7: 1) Downloading 'SRR3879849'... 2020-06-15T22:56:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:40 prefetch.2.10.7: 1) 'SRR3879849' was downloaded successfully Read 20752801 spots for SRR3879849/SRR3879849.sra Written 20752801 spots for SRR3879849/SRR3879849.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: 00:04:43 20752801 reads; of these: 20752801 (100.00%) were unpaired; of these: 2975654 (14.34%) aligned 0 times 14753410 (71.09%) aligned exactly 1 time 3023737 (14.57%) aligned >1 times 85.66% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 2463157 / 17777147 = 0.1386 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 08:07:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.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 08:07:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:03: 1000000 INFO @ Tue, 16 Jun 2020 08:08:09: 2000000 INFO @ Tue, 16 Jun 2020 08:08:14: 3000000 INFO @ Tue, 16 Jun 2020 08:08:19: 4000000 INFO @ Tue, 16 Jun 2020 08:08:25: 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 08:08:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.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 08:08:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:30: 6000000 INFO @ Tue, 16 Jun 2020 08:08:33: 1000000 INFO @ Tue, 16 Jun 2020 08:08:36: 7000000 INFO @ Tue, 16 Jun 2020 08:08:39: 2000000 INFO @ Tue, 16 Jun 2020 08:08:42: 8000000 INFO @ Tue, 16 Jun 2020 08:08:45: 3000000 INFO @ Tue, 16 Jun 2020 08:08:48: 9000000 INFO @ Tue, 16 Jun 2020 08:08:50: 4000000 INFO @ Tue, 16 Jun 2020 08:08:53: 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 08:08:56: 5000000 INFO @ Tue, 16 Jun 2020 08:08:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.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 08:08:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:59: 11000000 INFO @ Tue, 16 Jun 2020 08:09:02: 6000000 INFO @ Tue, 16 Jun 2020 08:09:04: 1000000 INFO @ Tue, 16 Jun 2020 08:09:05: 12000000 INFO @ Tue, 16 Jun 2020 08:09:08: 7000000 INFO @ Tue, 16 Jun 2020 08:09:11: 2000000 INFO @ Tue, 16 Jun 2020 08:09:11: 13000000 INFO @ Tue, 16 Jun 2020 08:09:14: 8000000 INFO @ Tue, 16 Jun 2020 08:09:17: 14000000 INFO @ Tue, 16 Jun 2020 08:09:17: 3000000 INFO @ Tue, 16 Jun 2020 08:09:20: 9000000 INFO @ Tue, 16 Jun 2020 08:09:23: 15000000 INFO @ Tue, 16 Jun 2020 08:09:24: 4000000 INFO @ Tue, 16 Jun 2020 08:09:25: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:09:25: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:09:25: #1 total tags in treatment: 15313990 INFO @ Tue, 16 Jun 2020 08:09:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:25: #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 08:09:25: #1 tags after filtering in treatment: 15313990 INFO @ Tue, 16 Jun 2020 08:09:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:26: 10000000 INFO @ Tue, 16 Jun 2020 08:09:26: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 08:09:26: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:26: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:09:26: #2 alternative fragment length(s) may be 1,41,492,598 bps INFO @ Tue, 16 Jun 2020 08:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.05_model.r WARNING @ Tue, 16 Jun 2020 08:09:26: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:26: #2 You may need to consider one of the other alternative d(s): 1,41,492,598 WARNING @ Tue, 16 Jun 2020 08:09:26: #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 08:09:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:30: 5000000 INFO @ Tue, 16 Jun 2020 08:09:32: 11000000 INFO @ Tue, 16 Jun 2020 08:09:37: 6000000 INFO @ Tue, 16 Jun 2020 08:09:38: 12000000 INFO @ Tue, 16 Jun 2020 08:09:43: 7000000 INFO @ Tue, 16 Jun 2020 08:09:45: 13000000 INFO @ Tue, 16 Jun 2020 08:09:50: 8000000 INFO @ Tue, 16 Jun 2020 08:09:51: 14000000 INFO @ Tue, 16 Jun 2020 08:09:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:56: 9000000 INFO @ Tue, 16 Jun 2020 08:09:57: 15000000 INFO @ Tue, 16 Jun 2020 08:09:59: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:09:59: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:09:59: #1 total tags in treatment: 15313990 INFO @ Tue, 16 Jun 2020 08:09:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:59: #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 08:09:59: #1 tags after filtering in treatment: 15313990 INFO @ Tue, 16 Jun 2020 08:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:00: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 08:10:00: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:01: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:10:01: #2 alternative fragment length(s) may be 1,41,492,598 bps INFO @ Tue, 16 Jun 2020 08:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.10_model.r WARNING @ Tue, 16 Jun 2020 08:10:01: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:01: #2 You may need to consider one of the other alternative d(s): 1,41,492,598 WARNING @ Tue, 16 Jun 2020 08:10:01: #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 08:10:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:02: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:10:09: 11000000 INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.05_summits.bed INFO @ Tue, 16 Jun 2020 08:10:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (697 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:15: 12000000 INFO @ Tue, 16 Jun 2020 08:10:21: 13000000 INFO @ Tue, 16 Jun 2020 08:10:27: 14000000 INFO @ Tue, 16 Jun 2020 08:10:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:34: 15000000 INFO @ Tue, 16 Jun 2020 08:10:36: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:10:36: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:10:36: #1 total tags in treatment: 15313990 INFO @ Tue, 16 Jun 2020 08:10:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:36: #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 08:10:36: #1 tags after filtering in treatment: 15313990 INFO @ Tue, 16 Jun 2020 08:10:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:37: #2 number of paired peaks: 289 WARNING @ Tue, 16 Jun 2020 08:10:37: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:37: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 08:10:37: #2 alternative fragment length(s) may be 1,41,492,598 bps INFO @ Tue, 16 Jun 2020 08:10:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.20_model.r WARNING @ Tue, 16 Jun 2020 08:10:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:37: #2 You may need to consider one of the other alternative d(s): 1,41,492,598 WARNING @ Tue, 16 Jun 2020 08:10:37: #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 08:10:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:10:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.10_summits.bed INFO @ Tue, 16 Jun 2020 08:10:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (408 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936242/SRX1936242.20_summits.bed INFO @ Tue, 16 Jun 2020 08:11:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (129 records, 4 fields): 1 millis CompletedMACS2peakCalling