Job ID = 16435506 SRX = SRX13110322 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: 00:04:35 14600942 reads; of these: 14600942 (100.00%) were unpaired; of these: 1850383 (12.67%) aligned 0 times 10816845 (74.08%) aligned exactly 1 time 1933714 (13.24%) aligned >1 times 87.33% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 1552903 / 12750559 = 0.1218 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 10:51:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.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 10:51:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:51:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:51:53: 1000000 INFO @ Tue, 02 Aug 2022 10:52:01: 2000000 INFO @ Tue, 02 Aug 2022 10:52:07: 3000000 INFO @ Tue, 02 Aug 2022 10:52:14: 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 10:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.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 10:52:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:52:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:21: 5000000 INFO @ Tue, 02 Aug 2022 10:52:24: 1000000 INFO @ Tue, 02 Aug 2022 10:52:29: 6000000 INFO @ Tue, 02 Aug 2022 10:52:32: 2000000 INFO @ Tue, 02 Aug 2022 10:52:37: 7000000 INFO @ Tue, 02 Aug 2022 10:52:39: 3000000 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 10:52:45: 8000000 INFO @ Tue, 02 Aug 2022 10:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.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 10:52:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:52:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:47: 4000000 INFO @ Tue, 02 Aug 2022 10:52:53: 9000000 INFO @ Tue, 02 Aug 2022 10:52:55: 1000000 INFO @ Tue, 02 Aug 2022 10:52:56: 5000000 INFO @ Tue, 02 Aug 2022 10:53:02: 10000000 INFO @ Tue, 02 Aug 2022 10:53:05: 6000000 INFO @ Tue, 02 Aug 2022 10:53:05: 2000000 INFO @ Tue, 02 Aug 2022 10:53:11: 11000000 INFO @ Tue, 02 Aug 2022 10:53:12: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:12: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:12: #1 total tags in treatment: 11197656 INFO @ Tue, 02 Aug 2022 10:53:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:12: #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 10:53:12: #1 tags after filtering in treatment: 11197656 INFO @ Tue, 02 Aug 2022 10:53:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:12: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:13: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 10:53:13: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 10:53:13: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:13: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:13: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:13: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:13: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:53:13: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.05_model.r WARNING @ Tue, 02 Aug 2022 10:53:13: #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 10:53:13: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:53:13: #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 10:53:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:53:13: 7000000 INFO @ Tue, 02 Aug 2022 10:53:15: 3000000 INFO @ Tue, 02 Aug 2022 10:53:22: 8000000 INFO @ Tue, 02 Aug 2022 10:53:25: 4000000 INFO @ Tue, 02 Aug 2022 10:53:31: 9000000 INFO @ Tue, 02 Aug 2022 10:53:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:53:35: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:53:39: 10000000 INFO @ Tue, 02 Aug 2022 10:53:44: 6000000 INFO @ Tue, 02 Aug 2022 10:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.05_summits.bed INFO @ Tue, 02 Aug 2022 10:53:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (759 records, 4 fields): 74 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:53:48: 11000000 INFO @ Tue, 02 Aug 2022 10:53:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:49: #1 total tags in treatment: 11197656 INFO @ Tue, 02 Aug 2022 10:53:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:49: #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 10:53:49: #1 tags after filtering in treatment: 11197656 INFO @ Tue, 02 Aug 2022 10:53:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:49: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:50: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 10:53:50: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 10:53:50: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:50: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:50: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:50: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:50: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:53:50: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:53:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.10_model.r WARNING @ Tue, 02 Aug 2022 10:53:50: #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 10:53:50: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:53:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:53:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:53:53: 7000000 INFO @ Tue, 02 Aug 2022 10:54:01: 8000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:54:09: 9000000 INFO @ Tue, 02 Aug 2022 10:54:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:17: 10000000 INFO @ Tue, 02 Aug 2022 10:54:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.10_summits.bed INFO @ Tue, 02 Aug 2022 10:54:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (416 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:54:25: 11000000 INFO @ Tue, 02 Aug 2022 10:54:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:54:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:54:27: #1 total tags in treatment: 11197656 INFO @ Tue, 02 Aug 2022 10:54:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:54:27: #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 10:54:27: #1 tags after filtering in treatment: 11197656 INFO @ Tue, 02 Aug 2022 10:54:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:54:27: #1 finished! INFO @ Tue, 02 Aug 2022 10:54:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:54:28: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 10:54:28: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 10:54:28: start model_add_line... INFO @ Tue, 02 Aug 2022 10:54:28: start X-correlation... INFO @ Tue, 02 Aug 2022 10:54:28: end of X-cor INFO @ Tue, 02 Aug 2022 10:54:28: #2 finished! INFO @ Tue, 02 Aug 2022 10:54:28: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:54:28: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.20_model.r WARNING @ Tue, 02 Aug 2022 10:54:28: #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 10:54:28: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:54:28: #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 10:54:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:54:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:54:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110322/SRX13110322.20_summits.bed INFO @ Tue, 02 Aug 2022 10:54:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (224 records, 4 fields): 49 millis CompletedMACS2peakCalling