Job ID = 6366895 SRX = SRX257640 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:23 prefetch.2.10.7: 1) Downloading 'SRR800649'... 2020-06-15T23:06:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:26 prefetch.2.10.7: 'SRR800649' is valid 2020-06-15T23:07:26 prefetch.2.10.7: 1) 'SRR800649' was downloaded successfully Read 10916207 spots for SRR800649/SRR800649.sra Written 10916207 spots for SRR800649/SRR800649.sra 2020-06-15T23:08:10 prefetch.2.10.7: 1) Downloading 'SRR800650'... 2020-06-15T23:08:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:09:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:09:35 prefetch.2.10.7: 'SRR800650' is valid 2020-06-15T23:09:35 prefetch.2.10.7: 1) 'SRR800650' was downloaded successfully Read 14166298 spots for SRR800650/SRR800650.sra Written 14166298 spots for SRR800650/SRR800650.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: 00:05:39 25082505 reads; of these: 25082505 (100.00%) were unpaired; of these: 4140777 (16.51%) aligned 0 times 17327008 (69.08%) aligned exactly 1 time 3614720 (14.41%) aligned >1 times 83.49% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 15208678 / 20941728 = 0.7262 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 08:20:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.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 08:20:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:44: 1000000 INFO @ Tue, 16 Jun 2020 08:20:50: 2000000 INFO @ Tue, 16 Jun 2020 08:20:57: 3000000 INFO @ Tue, 16 Jun 2020 08:21:03: 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 08:21:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.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 08:21:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:10: 5000000 INFO @ Tue, 16 Jun 2020 08:21:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:16: #1 total tags in treatment: 5733050 INFO @ Tue, 16 Jun 2020 08:21:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:16: #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 08:21:16: #1 tags after filtering in treatment: 5733050 INFO @ Tue, 16 Jun 2020 08:21:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:16: #2 number of paired peaks: 908 WARNING @ Tue, 16 Jun 2020 08:21:16: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:16: 1000000 INFO @ Tue, 16 Jun 2020 08:21:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:16: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:21:16: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.05_model.r WARNING @ Tue, 16 Jun 2020 08:21:17: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:17: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:21:17: #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 08:21:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:24: 2000000 INFO @ Tue, 16 Jun 2020 08:21:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:32: 3000000 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 08:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1376 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.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 08:21:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:40: 4000000 INFO @ Tue, 16 Jun 2020 08:21:46: 1000000 INFO @ Tue, 16 Jun 2020 08:21:49: 5000000 INFO @ Tue, 16 Jun 2020 08:21:54: 2000000 INFO @ Tue, 16 Jun 2020 08:21:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:21:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:21:56: #1 total tags in treatment: 5733050 INFO @ Tue, 16 Jun 2020 08:21:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:56: #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 08:21:56: #1 tags after filtering in treatment: 5733050 INFO @ Tue, 16 Jun 2020 08:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:56: #2 number of paired peaks: 908 WARNING @ Tue, 16 Jun 2020 08:21:56: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:56: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:21:56: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.10_model.r WARNING @ Tue, 16 Jun 2020 08:21:56: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:56: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:21:56: #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 08:21:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:02: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:10: 4000000 INFO @ Tue, 16 Jun 2020 08:22:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (839 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:18: 5000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:22:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:22:23: #1 total tags in treatment: 5733050 INFO @ Tue, 16 Jun 2020 08:22:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:23: #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 08:22:23: #1 tags after filtering in treatment: 5733050 INFO @ Tue, 16 Jun 2020 08:22:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:24: #2 number of paired peaks: 908 WARNING @ Tue, 16 Jun 2020 08:22:24: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Tue, 16 Jun 2020 08:22:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:24: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 08:22:24: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 16 Jun 2020 08:22:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.20_model.r WARNING @ Tue, 16 Jun 2020 08:22:24: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:22:24: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 16 Jun 2020 08:22:24: #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 08:22:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257640/SRX257640.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (452 records, 4 fields): 2 millis CompletedMACS2peakCalling