Job ID = 6366344 SRX = SRX118219 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:48:22 prefetch.2.10.7: 1) Downloading 'SRR403226'... 2020-06-15T22:48:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:00 prefetch.2.10.7: 'SRR403226' is valid 2020-06-15T22:49:00 prefetch.2.10.7: 1) 'SRR403226' was downloaded successfully Read 8331974 spots for SRR403226/SRR403226.sra Written 8331974 spots for SRR403226/SRR403226.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: 00:01:12 8331974 reads; of these: 8331974 (100.00%) were unpaired; of these: 384902 (4.62%) aligned 0 times 6699031 (80.40%) aligned exactly 1 time 1248041 (14.98%) aligned >1 times 95.38% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 668149 / 7947072 = 0.0841 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 07:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.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 07:52:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:41: 1000000 INFO @ Tue, 16 Jun 2020 07:52:47: 2000000 INFO @ Tue, 16 Jun 2020 07:52:53: 3000000 INFO @ Tue, 16 Jun 2020 07:52:59: 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 07:53:04: 5000000 INFO @ Tue, 16 Jun 2020 07:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.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 07:53:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:11: 1000000 INFO @ Tue, 16 Jun 2020 07:53:11: 6000000 INFO @ Tue, 16 Jun 2020 07:53:16: 2000000 INFO @ Tue, 16 Jun 2020 07:53:17: 7000000 INFO @ Tue, 16 Jun 2020 07:53:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:53:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:53:18: #1 total tags in treatment: 7278923 INFO @ Tue, 16 Jun 2020 07:53:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:18: #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 07:53:19: #1 tags after filtering in treatment: 7278923 INFO @ Tue, 16 Jun 2020 07:53:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:19: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 07:53:19: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:19: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:53:19: #2 alternative fragment length(s) may be 3,36 bps INFO @ Tue, 16 Jun 2020 07:53:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.05_model.r WARNING @ Tue, 16 Jun 2020 07:53:19: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:19: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Tue, 16 Jun 2020 07:53:19: #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 07:53:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:22: 3000000 INFO @ Tue, 16 Jun 2020 07:53:27: 4000000 INFO @ Tue, 16 Jun 2020 07:53:32: 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 07:53:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.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 07:53:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:37: 6000000 INFO @ Tue, 16 Jun 2020 07:53:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (468 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:41: 1000000 INFO @ Tue, 16 Jun 2020 07:53:43: 7000000 INFO @ Tue, 16 Jun 2020 07:53:44: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:53:44: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:53:44: #1 total tags in treatment: 7278923 INFO @ Tue, 16 Jun 2020 07:53:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:44: #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 07:53:45: #1 tags after filtering in treatment: 7278923 INFO @ Tue, 16 Jun 2020 07:53:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:45: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:45: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 07:53:45: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:45: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:45: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:45: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:45: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:45: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:53:45: #2 alternative fragment length(s) may be 3,36 bps INFO @ Tue, 16 Jun 2020 07:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.10_model.r WARNING @ Tue, 16 Jun 2020 07:53:45: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:53:45: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Tue, 16 Jun 2020 07:53:45: #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 07:53:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:47: 2000000 INFO @ Tue, 16 Jun 2020 07:53:53: 3000000 INFO @ Tue, 16 Jun 2020 07:53:59: 4000000 INFO @ Tue, 16 Jun 2020 07:53:59: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:54:05: 5000000 INFO @ Tue, 16 Jun 2020 07:54:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.10_summits.bed INFO @ Tue, 16 Jun 2020 07:54:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:54:10: 6000000 INFO @ Tue, 16 Jun 2020 07:54:16: 7000000 INFO @ Tue, 16 Jun 2020 07:54:18: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:54:18: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:54:18: #1 total tags in treatment: 7278923 INFO @ Tue, 16 Jun 2020 07:54:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:18: #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 07:54:18: #1 tags after filtering in treatment: 7278923 INFO @ Tue, 16 Jun 2020 07:54:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:18: #2 number of paired peaks: 333 WARNING @ Tue, 16 Jun 2020 07:54:18: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:18: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:18: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:18: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:18: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:18: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 07:54:18: #2 alternative fragment length(s) may be 3,36 bps INFO @ Tue, 16 Jun 2020 07:54:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.20_model.r WARNING @ Tue, 16 Jun 2020 07:54:18: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:54:18: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Tue, 16 Jun 2020 07:54:18: #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 07:54:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX118219/SRX118219.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling