Job ID = 6368475 SRX = SRX5020705 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:16 prefetch.2.10.7: 1) Downloading 'SRR8201328'... 2020-06-16T00:26:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:27 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:28 prefetch.2.10.7: 'SRR8201328' is valid 2020-06-16T00:27:28 prefetch.2.10.7: 1) 'SRR8201328' was downloaded successfully Read 9986477 spots for SRR8201328/SRR8201328.sra Written 9986477 spots for SRR8201328/SRR8201328.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: 00:02:23 9986477 reads; of these: 9986477 (100.00%) were unpaired; of these: 102336 (1.02%) aligned 0 times 8267267 (82.78%) aligned exactly 1 time 1616874 (16.19%) aligned >1 times 98.98% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 675929 / 9884141 = 0.0684 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 09:33:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.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 09:33:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:25: 1000000 INFO @ Tue, 16 Jun 2020 09:33:30: 2000000 INFO @ Tue, 16 Jun 2020 09:33:35: 3000000 INFO @ Tue, 16 Jun 2020 09:33:40: 4000000 INFO @ Tue, 16 Jun 2020 09:33:45: 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 09:33:49: 6000000 INFO @ Tue, 16 Jun 2020 09:33:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.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 09:33:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:54: 7000000 INFO @ Tue, 16 Jun 2020 09:33:56: 1000000 INFO @ Tue, 16 Jun 2020 09:33:59: 8000000 INFO @ Tue, 16 Jun 2020 09:34:01: 2000000 INFO @ Tue, 16 Jun 2020 09:34:04: 9000000 INFO @ Tue, 16 Jun 2020 09:34:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:05: #1 total tags in treatment: 9208212 INFO @ Tue, 16 Jun 2020 09:34:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:05: #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 09:34:05: #1 tags after filtering in treatment: 9208212 INFO @ Tue, 16 Jun 2020 09:34:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:06: 3000000 INFO @ Tue, 16 Jun 2020 09:34:06: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 09:34:06: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:06: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:34:06: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:34:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.05_model.r WARNING @ Tue, 16 Jun 2020 09:34:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:06: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:34:06: #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 09:34:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:11: 4000000 INFO @ Tue, 16 Jun 2020 09:34:16: 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 09:34:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.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 09:34:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:21: 6000000 INFO @ Tue, 16 Jun 2020 09:34:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:26: 1000000 INFO @ Tue, 16 Jun 2020 09:34:26: 7000000 INFO @ Tue, 16 Jun 2020 09:34:31: 2000000 INFO @ Tue, 16 Jun 2020 09:34:31: 8000000 INFO @ Tue, 16 Jun 2020 09:34:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.05_summits.bed INFO @ Tue, 16 Jun 2020 09:34:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:36: 3000000 INFO @ Tue, 16 Jun 2020 09:34:36: 9000000 INFO @ Tue, 16 Jun 2020 09:34:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:37: #1 total tags in treatment: 9208212 INFO @ Tue, 16 Jun 2020 09:34:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:37: #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 09:34:37: #1 tags after filtering in treatment: 9208212 INFO @ Tue, 16 Jun 2020 09:34:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:38: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 09:34:38: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:38: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:34:38: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.10_model.r WARNING @ Tue, 16 Jun 2020 09:34:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:38: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:34:38: #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 09:34:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:41: 4000000 INFO @ Tue, 16 Jun 2020 09:34:46: 5000000 INFO @ Tue, 16 Jun 2020 09:34:50: 6000000 INFO @ Tue, 16 Jun 2020 09:34:55: 7000000 INFO @ Tue, 16 Jun 2020 09:34:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:00: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:05: 9000000 INFO @ Tue, 16 Jun 2020 09:35:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:06: #1 total tags in treatment: 9208212 INFO @ Tue, 16 Jun 2020 09:35:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:06: #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 09:35:06: #1 tags after filtering in treatment: 9208212 INFO @ Tue, 16 Jun 2020 09:35:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:07: #2 number of paired peaks: 270 WARNING @ Tue, 16 Jun 2020 09:35:07: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:07: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:35:07: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:35:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:07: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:07: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:35:07: #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 09:35:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:35:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020705/SRX5020705.20_summits.bed INFO @ Tue, 16 Jun 2020 09:35:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 1 millis CompletedMACS2peakCalling