Job ID = 14160697 SRX = SRX10399020 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:01:44 9344915 reads; of these: 9344915 (100.00%) were unpaired; of these: 2520557 (26.97%) aligned 0 times 5675712 (60.74%) aligned exactly 1 time 1148646 (12.29%) aligned >1 times 73.03% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 535306 / 6824358 = 0.0784 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.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 @ Thu, 09 Dec 2021 03:49:59: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:49:59: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:50:04: 1000000 INFO @ Thu, 09 Dec 2021 03:50:10: 2000000 INFO @ Thu, 09 Dec 2021 03:50:16: 3000000 INFO @ Thu, 09 Dec 2021 03:50:22: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:50:27: 5000000 INFO @ Thu, 09 Dec 2021 03:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.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 @ Thu, 09 Dec 2021 03:50:29: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:50:29: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:50:33: 6000000 INFO @ Thu, 09 Dec 2021 03:50:35: 1000000 INFO @ Thu, 09 Dec 2021 03:50:35: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:50:35: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:50:35: #1 total tags in treatment: 6289052 INFO @ Thu, 09 Dec 2021 03:50:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:50:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:50:35: #1 tags after filtering in treatment: 6289052 INFO @ Thu, 09 Dec 2021 03:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:50:35: #1 finished! INFO @ Thu, 09 Dec 2021 03:50:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:50:36: #2 number of paired peaks: 578 WARNING @ Thu, 09 Dec 2021 03:50:36: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Thu, 09 Dec 2021 03:50:36: start model_add_line... INFO @ Thu, 09 Dec 2021 03:50:36: start X-correlation... INFO @ Thu, 09 Dec 2021 03:50:36: end of X-cor INFO @ Thu, 09 Dec 2021 03:50:36: #2 finished! INFO @ Thu, 09 Dec 2021 03:50:36: #2 predicted fragment length is 93 bps INFO @ Thu, 09 Dec 2021 03:50:36: #2 alternative fragment length(s) may be 93 bps INFO @ Thu, 09 Dec 2021 03:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.05_model.r WARNING @ Thu, 09 Dec 2021 03:50:36: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:50:36: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Thu, 09 Dec 2021 03:50:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:50:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:50:41: 2000000 INFO @ Thu, 09 Dec 2021 03:50:47: 3000000 INFO @ Thu, 09 Dec 2021 03:50:48: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:50:53: 4000000 INFO @ Thu, 09 Dec 2021 03:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.05_summits.bed INFO @ Thu, 09 Dec 2021 03:50:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1035 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 03:50:58: 5000000 INFO @ Thu, 09 Dec 2021 03:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.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 @ Thu, 09 Dec 2021 03:50:59: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:50:59: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:51:04: 6000000 INFO @ Thu, 09 Dec 2021 03:51:05: 1000000 INFO @ Thu, 09 Dec 2021 03:51:06: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:51:06: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:51:06: #1 total tags in treatment: 6289052 INFO @ Thu, 09 Dec 2021 03:51:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:51:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:51:06: #1 tags after filtering in treatment: 6289052 INFO @ Thu, 09 Dec 2021 03:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:51:06: #1 finished! INFO @ Thu, 09 Dec 2021 03:51:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:51:07: #2 number of paired peaks: 578 WARNING @ Thu, 09 Dec 2021 03:51:07: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Thu, 09 Dec 2021 03:51:07: start model_add_line... INFO @ Thu, 09 Dec 2021 03:51:07: start X-correlation... INFO @ Thu, 09 Dec 2021 03:51:07: end of X-cor INFO @ Thu, 09 Dec 2021 03:51:07: #2 finished! INFO @ Thu, 09 Dec 2021 03:51:07: #2 predicted fragment length is 93 bps INFO @ Thu, 09 Dec 2021 03:51:07: #2 alternative fragment length(s) may be 93 bps INFO @ Thu, 09 Dec 2021 03:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.10_model.r WARNING @ Thu, 09 Dec 2021 03:51:07: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:51:07: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Thu, 09 Dec 2021 03:51:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:51:07: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:51:11: 2000000 INFO @ Thu, 09 Dec 2021 03:51:17: 3000000 INFO @ Thu, 09 Dec 2021 03:51:20: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:51:22: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:51:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:51:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:51:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.10_summits.bed INFO @ Thu, 09 Dec 2021 03:51:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (694 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:51:28: 5000000 INFO @ Thu, 09 Dec 2021 03:51:34: 6000000 INFO @ Thu, 09 Dec 2021 03:51:36: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:51:36: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:51:36: #1 total tags in treatment: 6289052 INFO @ Thu, 09 Dec 2021 03:51:36: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:51:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:51:36: #1 tags after filtering in treatment: 6289052 INFO @ Thu, 09 Dec 2021 03:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:51:36: #1 finished! INFO @ Thu, 09 Dec 2021 03:51:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:51:36: #2 number of paired peaks: 578 WARNING @ Thu, 09 Dec 2021 03:51:36: Fewer paired peaks (578) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 578 pairs to build model! INFO @ Thu, 09 Dec 2021 03:51:36: start model_add_line... INFO @ Thu, 09 Dec 2021 03:51:36: start X-correlation... INFO @ Thu, 09 Dec 2021 03:51:36: end of X-cor INFO @ Thu, 09 Dec 2021 03:51:36: #2 finished! INFO @ Thu, 09 Dec 2021 03:51:36: #2 predicted fragment length is 93 bps INFO @ Thu, 09 Dec 2021 03:51:36: #2 alternative fragment length(s) may be 93 bps INFO @ Thu, 09 Dec 2021 03:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.20_model.r WARNING @ Thu, 09 Dec 2021 03:51:36: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:51:36: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Thu, 09 Dec 2021 03:51:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:51:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:51:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:51:49: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:51:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:51:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:51:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10399020/SRX10399020.20_summits.bed INFO @ Thu, 09 Dec 2021 03:51:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (302 records, 4 fields): 12 millis CompletedMACS2peakCalling