Job ID = 16434855 SRX = SRX10435508 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: 00:02:10 6835838 reads; of these: 6835838 (100.00%) were unpaired; of these: 1824884 (26.70%) aligned 0 times 4123778 (60.33%) aligned exactly 1 time 887176 (12.98%) aligned >1 times 73.30% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 403231 / 5010954 = 0.0805 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.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, 02 Aug 2022 10:06:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:06:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:06:36: 1000000 INFO @ Tue, 02 Aug 2022 10:06:42: 2000000 INFO @ Tue, 02 Aug 2022 10:06:48: 3000000 INFO @ Tue, 02 Aug 2022 10:06:54: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:06:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.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, 02 Aug 2022 10:06:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:06:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:06:58: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:06:58: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:06:58: #1 total tags in treatment: 4607723 INFO @ Tue, 02 Aug 2022 10:06:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:06:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:06:58: #1 tags after filtering in treatment: 4607723 INFO @ Tue, 02 Aug 2022 10:06:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:06:58: #1 finished! INFO @ Tue, 02 Aug 2022 10:06:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:06:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:06:59: #2 number of paired peaks: 400 WARNING @ Tue, 02 Aug 2022 10:06:59: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Tue, 02 Aug 2022 10:06:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:06:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:06:59: end of X-cor INFO @ Tue, 02 Aug 2022 10:06:59: #2 finished! INFO @ Tue, 02 Aug 2022 10:06:59: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:06:59: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 10:06:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.05_model.r WARNING @ Tue, 02 Aug 2022 10:06:59: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:06:59: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 10:06:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:06:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:06:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:07:04: 1000000 INFO @ Tue, 02 Aug 2022 10:07:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:07:10: 2000000 INFO @ Tue, 02 Aug 2022 10:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:07:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:07:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.05_summits.bed INFO @ Tue, 02 Aug 2022 10:07:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:07:15: 3000000 INFO @ Tue, 02 Aug 2022 10:07:21: 4000000 INFO @ Tue, 02 Aug 2022 10:07:24: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:07:24: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:07:24: #1 total tags in treatment: 4607723 INFO @ Tue, 02 Aug 2022 10:07:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:07:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:07:24: #1 tags after filtering in treatment: 4607723 INFO @ Tue, 02 Aug 2022 10:07:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:07:24: #1 finished! INFO @ Tue, 02 Aug 2022 10:07:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:07:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:07:25: #2 number of paired peaks: 400 WARNING @ Tue, 02 Aug 2022 10:07:25: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Tue, 02 Aug 2022 10:07:25: start model_add_line... INFO @ Tue, 02 Aug 2022 10:07:25: start X-correlation... INFO @ Tue, 02 Aug 2022 10:07:25: end of X-cor INFO @ Tue, 02 Aug 2022 10:07:25: #2 finished! INFO @ Tue, 02 Aug 2022 10:07:25: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:07:25: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 10:07:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.10_model.r WARNING @ Tue, 02 Aug 2022 10:07:25: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:07:25: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 10:07:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:07:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:07:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.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, 02 Aug 2022 10:07:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:07:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:07:34: 1000000 INFO @ Tue, 02 Aug 2022 10:07:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:07:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:07:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:07:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.10_summits.bed INFO @ Tue, 02 Aug 2022 10:07:40: Done! INFO @ Tue, 02 Aug 2022 10:07:40: 2000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (309 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:07:46: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:07:52: 4000000 INFO @ Tue, 02 Aug 2022 10:07:56: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:07:56: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:07:56: #1 total tags in treatment: 4607723 INFO @ Tue, 02 Aug 2022 10:07:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:07:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:07:56: #1 tags after filtering in treatment: 4607723 INFO @ Tue, 02 Aug 2022 10:07:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:07:56: #1 finished! INFO @ Tue, 02 Aug 2022 10:07:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:07:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:07:57: #2 number of paired peaks: 400 WARNING @ Tue, 02 Aug 2022 10:07:57: Fewer paired peaks (400) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 400 pairs to build model! INFO @ Tue, 02 Aug 2022 10:07:57: start model_add_line... INFO @ Tue, 02 Aug 2022 10:07:57: start X-correlation... INFO @ Tue, 02 Aug 2022 10:07:57: end of X-cor INFO @ Tue, 02 Aug 2022 10:07:57: #2 finished! INFO @ Tue, 02 Aug 2022 10:07:57: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:07:57: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 10:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.20_model.r WARNING @ Tue, 02 Aug 2022 10:07:57: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:07:57: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 10:07:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:07:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:07:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:08:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:08:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:08:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:08:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435508/SRX10435508.20_summits.bed INFO @ Tue, 02 Aug 2022 10:08:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 21 millis CompletedMACS2peakCalling