Job ID = 16435011 SRX = SRX10435538 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: 00:01:55 9247970 reads; of these: 9247970 (100.00%) were unpaired; of these: 77519 (0.84%) aligned 0 times 7729780 (83.58%) aligned exactly 1 time 1440671 (15.58%) aligned >1 times 99.16% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 618467 / 9170451 = 0.0674 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 10:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.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 10:35:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:35:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:35:29: 1000000 INFO @ Tue, 02 Aug 2022 10:35:36: 2000000 INFO @ Tue, 02 Aug 2022 10:35:44: 3000000 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 10:35:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.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 10:35:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:35:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:35:52: 4000000 INFO @ Tue, 02 Aug 2022 10:35:58: 1000000 INFO @ Tue, 02 Aug 2022 10:36:00: 5000000 INFO @ Tue, 02 Aug 2022 10:36:05: 2000000 INFO @ Tue, 02 Aug 2022 10:36:08: 6000000 INFO @ Tue, 02 Aug 2022 10:36:13: 3000000 INFO @ Tue, 02 Aug 2022 10:36:16: 7000000 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 10:36:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.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 10:36:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:36:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:36:21: 4000000 INFO @ Tue, 02 Aug 2022 10:36:23: 8000000 INFO @ Tue, 02 Aug 2022 10:36:27: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:36:27: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:36:27: #1 total tags in treatment: 8551984 INFO @ Tue, 02 Aug 2022 10:36:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:36:27: #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 10:36:27: #1 tags after filtering in treatment: 8551984 INFO @ Tue, 02 Aug 2022 10:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:36:27: #1 finished! INFO @ Tue, 02 Aug 2022 10:36:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:36:28: #2 number of paired peaks: 303 WARNING @ Tue, 02 Aug 2022 10:36:28: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 02 Aug 2022 10:36:28: start model_add_line... INFO @ Tue, 02 Aug 2022 10:36:28: 1000000 INFO @ Tue, 02 Aug 2022 10:36:28: start X-correlation... INFO @ Tue, 02 Aug 2022 10:36:28: end of X-cor INFO @ Tue, 02 Aug 2022 10:36:28: #2 finished! INFO @ Tue, 02 Aug 2022 10:36:28: #2 predicted fragment length is 52 bps INFO @ Tue, 02 Aug 2022 10:36:28: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 02 Aug 2022 10:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.05_model.r WARNING @ Tue, 02 Aug 2022 10:36:28: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:36:28: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 02 Aug 2022 10:36:28: #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 10:36:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:36:28: 5000000 INFO @ Tue, 02 Aug 2022 10:36:36: 6000000 INFO @ Tue, 02 Aug 2022 10:36:36: 2000000 INFO @ Tue, 02 Aug 2022 10:36:43: 7000000 INFO @ Tue, 02 Aug 2022 10:36:44: 3000000 INFO @ Tue, 02 Aug 2022 10:36:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:36:50: 8000000 INFO @ Tue, 02 Aug 2022 10:36:52: 4000000 INFO @ Tue, 02 Aug 2022 10:36:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:36:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:36:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.05_summits.bed INFO @ Tue, 02 Aug 2022 10:36:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (534 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:36:54: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:36:54: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:36:54: #1 total tags in treatment: 8551984 INFO @ Tue, 02 Aug 2022 10:36:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:36:54: #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 10:36:54: #1 tags after filtering in treatment: 8551984 INFO @ Tue, 02 Aug 2022 10:36:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:36:54: #1 finished! INFO @ Tue, 02 Aug 2022 10:36:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:36:55: #2 number of paired peaks: 303 WARNING @ Tue, 02 Aug 2022 10:36:55: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 02 Aug 2022 10:36:55: start model_add_line... INFO @ Tue, 02 Aug 2022 10:36:55: start X-correlation... INFO @ Tue, 02 Aug 2022 10:36:55: end of X-cor INFO @ Tue, 02 Aug 2022 10:36:55: #2 finished! INFO @ Tue, 02 Aug 2022 10:36:55: #2 predicted fragment length is 52 bps INFO @ Tue, 02 Aug 2022 10:36:55: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 02 Aug 2022 10:36:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.10_model.r WARNING @ Tue, 02 Aug 2022 10:36:55: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:36:55: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 02 Aug 2022 10:36:55: #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 10:36:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:36:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:36:59: 5000000 INFO @ Tue, 02 Aug 2022 10:37:07: 6000000 INFO @ Tue, 02 Aug 2022 10:37:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:37:13: 7000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:37:20: 8000000 INFO @ Tue, 02 Aug 2022 10:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.10_summits.bed INFO @ Tue, 02 Aug 2022 10:37:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (311 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:37:23: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:37:23: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:37:23: #1 total tags in treatment: 8551984 INFO @ Tue, 02 Aug 2022 10:37:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:37:23: #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 10:37:23: #1 tags after filtering in treatment: 8551984 INFO @ Tue, 02 Aug 2022 10:37:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:37:23: #1 finished! INFO @ Tue, 02 Aug 2022 10:37:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:37:24: #2 number of paired peaks: 303 WARNING @ Tue, 02 Aug 2022 10:37:24: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Tue, 02 Aug 2022 10:37:24: start model_add_line... INFO @ Tue, 02 Aug 2022 10:37:24: start X-correlation... INFO @ Tue, 02 Aug 2022 10:37:24: end of X-cor INFO @ Tue, 02 Aug 2022 10:37:24: #2 finished! INFO @ Tue, 02 Aug 2022 10:37:24: #2 predicted fragment length is 52 bps INFO @ Tue, 02 Aug 2022 10:37:24: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 02 Aug 2022 10:37:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.20_model.r WARNING @ Tue, 02 Aug 2022 10:37:24: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:37:24: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 02 Aug 2022 10:37:24: #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 10:37:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:37:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:37:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435538/SRX10435538.20_summits.bed INFO @ Tue, 02 Aug 2022 10:37:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (118 records, 4 fields): 36 millis CompletedMACS2peakCalling