Job ID = 6367757 SRX = SRX4082371 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:35 prefetch.2.10.7: 1) Downloading 'SRR7164189'... 2020-06-15T23:34:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:19 prefetch.2.10.7: 'SRR7164189' is valid 2020-06-15T23:35:19 prefetch.2.10.7: 1) 'SRR7164189' was downloaded successfully 2020-06-15T23:35:19 prefetch.2.10.7: 'SRR7164189' has 0 unresolved dependencies Read 11730132 spots for SRR7164189/SRR7164189.sra Written 11730132 spots for SRR7164189/SRR7164189.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: 00:01:11 11730132 reads; of these: 11730132 (100.00%) were unpaired; of these: 4516721 (38.51%) aligned 0 times 5543864 (47.26%) aligned exactly 1 time 1669547 (14.23%) aligned >1 times 61.49% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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_rmdupse_core] 1110269 / 7213411 = 0.1539 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 08:38:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.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 08:38:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:50: 1000000 INFO @ Tue, 16 Jun 2020 08:38:55: 2000000 INFO @ Tue, 16 Jun 2020 08:39:00: 3000000 INFO @ Tue, 16 Jun 2020 08:39:05: 4000000 INFO @ Tue, 16 Jun 2020 08:39:09: 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 08:39:14: 6000000 INFO @ Tue, 16 Jun 2020 08:39:15: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:39:15: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:39:15: #1 total tags in treatment: 6103142 INFO @ Tue, 16 Jun 2020 08:39:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:15: #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 08:39:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.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 08:39:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:15: #1 tags after filtering in treatment: 6103142 INFO @ Tue, 16 Jun 2020 08:39:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:15: #2 number of paired peaks: 291 WARNING @ Tue, 16 Jun 2020 08:39:15: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:15: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:39:15: #2 alternative fragment length(s) may be 1,30,69,91,117,547,572 bps INFO @ Tue, 16 Jun 2020 08:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.05_model.r WARNING @ Tue, 16 Jun 2020 08:39:15: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:15: #2 You may need to consider one of the other alternative d(s): 1,30,69,91,117,547,572 WARNING @ Tue, 16 Jun 2020 08:39:15: #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 08:39:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:20: 1000000 INFO @ Tue, 16 Jun 2020 08:39:24: 2000000 INFO @ Tue, 16 Jun 2020 08:39:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:29: 3000000 INFO @ Tue, 16 Jun 2020 08:39:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.05_summits.bed INFO @ Tue, 16 Jun 2020 08:39:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:39:34: 4000000 INFO @ Tue, 16 Jun 2020 08:39:39: 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 08:39:44: 6000000 INFO @ Tue, 16 Jun 2020 08:39:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:39:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:39:44: #1 total tags in treatment: 6103142 INFO @ Tue, 16 Jun 2020 08:39:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:44: #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 08:39:44: #1 tags after filtering in treatment: 6103142 INFO @ Tue, 16 Jun 2020 08:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:44: #2 number of paired peaks: 291 WARNING @ Tue, 16 Jun 2020 08:39:44: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:45: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:39:45: #2 alternative fragment length(s) may be 1,30,69,91,117,547,572 bps INFO @ Tue, 16 Jun 2020 08:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.10_model.r WARNING @ Tue, 16 Jun 2020 08:39:45: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:45: #2 You may need to consider one of the other alternative d(s): 1,30,69,91,117,547,572 WARNING @ Tue, 16 Jun 2020 08:39:45: #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 08:39:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.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 08:39:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:50: 1000000 INFO @ Tue, 16 Jun 2020 08:39:55: 2000000 INFO @ Tue, 16 Jun 2020 08:39:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:59: 3000000 INFO @ Tue, 16 Jun 2020 08:40:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.10_summits.bed INFO @ Tue, 16 Jun 2020 08:40:03: Done! INFO @ Tue, 16 Jun 2020 08:40:04: 4000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (114 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:09: 5000000 INFO @ Tue, 16 Jun 2020 08:40:14: 6000000 INFO @ Tue, 16 Jun 2020 08:40:14: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:40:14: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:40:14: #1 total tags in treatment: 6103142 INFO @ Tue, 16 Jun 2020 08:40:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:14: #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 08:40:14: #1 tags after filtering in treatment: 6103142 INFO @ Tue, 16 Jun 2020 08:40:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:14: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:15: #2 number of paired peaks: 291 WARNING @ Tue, 16 Jun 2020 08:40:15: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:15: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:40:15: #2 alternative fragment length(s) may be 1,30,69,91,117,547,572 bps INFO @ Tue, 16 Jun 2020 08:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.20_model.r WARNING @ Tue, 16 Jun 2020 08:40:15: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:15: #2 You may need to consider one of the other alternative d(s): 1,30,69,91,117,547,572 WARNING @ Tue, 16 Jun 2020 08:40:15: #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 08:40:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082371/SRX4082371.20_summits.bed INFO @ Tue, 16 Jun 2020 08:40:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling