Job ID = 6368677 SRX = SRX5402704 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:16 prefetch.2.10.7: 1) Downloading 'SRR8602938'... 2020-06-16T00:25:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:51 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:52 prefetch.2.10.7: 'SRR8602938' is valid 2020-06-16T00:26:52 prefetch.2.10.7: 1) 'SRR8602938' was downloaded successfully 2020-06-16T00:26:52 prefetch.2.10.7: 'SRR8602938' has 0 unresolved dependencies Read 19023518 spots for SRR8602938/SRR8602938.sra Written 19023518 spots for SRR8602938/SRR8602938.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: 00:04:14 19023518 reads; of these: 19023518 (100.00%) were unpaired; of these: 184926 (0.97%) aligned 0 times 14195534 (74.62%) aligned exactly 1 time 4643058 (24.41%) aligned >1 times 99.03% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 8697731 / 18838592 = 0.4617 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 09:36:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.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 09:36:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:05: 1000000 INFO @ Tue, 16 Jun 2020 09:36:10: 2000000 INFO @ Tue, 16 Jun 2020 09:36:15: 3000000 INFO @ Tue, 16 Jun 2020 09:36:20: 4000000 INFO @ Tue, 16 Jun 2020 09:36:25: 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 09:36:30: 6000000 INFO @ Tue, 16 Jun 2020 09:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.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 09:36:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:35: 7000000 INFO @ Tue, 16 Jun 2020 09:36:36: 1000000 INFO @ Tue, 16 Jun 2020 09:36:40: 8000000 INFO @ Tue, 16 Jun 2020 09:36:41: 2000000 INFO @ Tue, 16 Jun 2020 09:36:45: 9000000 INFO @ Tue, 16 Jun 2020 09:36:46: 3000000 INFO @ Tue, 16 Jun 2020 09:36:51: 10000000 INFO @ Tue, 16 Jun 2020 09:36:51: 4000000 INFO @ Tue, 16 Jun 2020 09:36:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:51: #1 total tags in treatment: 10140861 INFO @ Tue, 16 Jun 2020 09:36:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:51: #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 09:36:51: #1 tags after filtering in treatment: 10140861 INFO @ Tue, 16 Jun 2020 09:36:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:52: #2 number of paired peaks: 795 WARNING @ Tue, 16 Jun 2020 09:36:52: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:52: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:36:52: #2 alternative fragment length(s) may be 3,53 bps INFO @ Tue, 16 Jun 2020 09:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:52: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Tue, 16 Jun 2020 09:36:52: #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 09:36:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:56: 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 09:37:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.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 09:37:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:01: 6000000 INFO @ Tue, 16 Jun 2020 09:37:05: 1000000 INFO @ Tue, 16 Jun 2020 09:37:05: 7000000 INFO @ Tue, 16 Jun 2020 09:37:10: 2000000 INFO @ Tue, 16 Jun 2020 09:37:10: 8000000 INFO @ Tue, 16 Jun 2020 09:37:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:15: 3000000 INFO @ Tue, 16 Jun 2020 09:37:15: 9000000 INFO @ Tue, 16 Jun 2020 09:37:20: 4000000 INFO @ Tue, 16 Jun 2020 09:37:20: 10000000 INFO @ Tue, 16 Jun 2020 09:37:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:21: #1 total tags in treatment: 10140861 INFO @ Tue, 16 Jun 2020 09:37:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:21: #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 09:37:21: #1 tags after filtering in treatment: 10140861 INFO @ Tue, 16 Jun 2020 09:37:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1762 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:22: #2 number of paired peaks: 795 WARNING @ Tue, 16 Jun 2020 09:37:22: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:22: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:37:22: #2 alternative fragment length(s) may be 3,53 bps INFO @ Tue, 16 Jun 2020 09:37:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.10_model.r WARNING @ Tue, 16 Jun 2020 09:37:22: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:22: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Tue, 16 Jun 2020 09:37:22: #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 09:37:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:25: 5000000 INFO @ Tue, 16 Jun 2020 09:37:29: 6000000 INFO @ Tue, 16 Jun 2020 09:37:34: 7000000 INFO @ Tue, 16 Jun 2020 09:37:39: 8000000 INFO @ Tue, 16 Jun 2020 09:37:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:44: 9000000 INFO @ Tue, 16 Jun 2020 09:37:49: 10000000 INFO @ Tue, 16 Jun 2020 09:37:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:49: #1 total tags in treatment: 10140861 INFO @ Tue, 16 Jun 2020 09:37:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:49: #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 09:37:49: #1 tags after filtering in treatment: 10140861 INFO @ Tue, 16 Jun 2020 09:37:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (745 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:50: #2 number of paired peaks: 795 WARNING @ Tue, 16 Jun 2020 09:37:50: Fewer paired peaks (795) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 795 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:50: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:37:50: #2 alternative fragment length(s) may be 3,53 bps INFO @ Tue, 16 Jun 2020 09:37:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:50: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Tue, 16 Jun 2020 09:37:50: #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 09:37:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:38:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402704/SRX5402704.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (271 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。