Job ID = 16436159 SRX = SRX13110362 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: 00:06:47 24225733 reads; of these: 24225733 (100.00%) were unpaired; of these: 2642454 (10.91%) aligned 0 times 18088431 (74.67%) aligned exactly 1 time 3494848 (14.43%) aligned >1 times 89.09% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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 12 files... [bam_rmdupse_core] 2532787 / 21583279 = 0.1173 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 11:11:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.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 11:11:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:11:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:11:57: 1000000 INFO @ Tue, 02 Aug 2022 11:12:02: 2000000 INFO @ Tue, 02 Aug 2022 11:12:07: 3000000 INFO @ Tue, 02 Aug 2022 11:12:12: 4000000 INFO @ Tue, 02 Aug 2022 11:12:17: 5000000 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 11:12:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.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 11:12:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:12:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:12:22: 6000000 INFO @ Tue, 02 Aug 2022 11:12:28: 7000000 INFO @ Tue, 02 Aug 2022 11:12:28: 1000000 INFO @ Tue, 02 Aug 2022 11:12:33: 8000000 INFO @ Tue, 02 Aug 2022 11:12:34: 2000000 INFO @ Tue, 02 Aug 2022 11:12:39: 9000000 INFO @ Tue, 02 Aug 2022 11:12:41: 3000000 INFO @ Tue, 02 Aug 2022 11:12:45: 10000000 INFO @ Tue, 02 Aug 2022 11:12:48: 4000000 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 11:12:50: 11000000 INFO @ Tue, 02 Aug 2022 11:12:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.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 11:12:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:12:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:12:54: 5000000 INFO @ Tue, 02 Aug 2022 11:12:56: 12000000 INFO @ Tue, 02 Aug 2022 11:12:57: 1000000 INFO @ Tue, 02 Aug 2022 11:13:00: 6000000 INFO @ Tue, 02 Aug 2022 11:13:02: 13000000 INFO @ Tue, 02 Aug 2022 11:13:03: 2000000 INFO @ Tue, 02 Aug 2022 11:13:06: 7000000 INFO @ Tue, 02 Aug 2022 11:13:07: 14000000 INFO @ Tue, 02 Aug 2022 11:13:08: 3000000 INFO @ Tue, 02 Aug 2022 11:13:13: 8000000 INFO @ Tue, 02 Aug 2022 11:13:13: 15000000 INFO @ Tue, 02 Aug 2022 11:13:14: 4000000 INFO @ Tue, 02 Aug 2022 11:13:19: 16000000 INFO @ Tue, 02 Aug 2022 11:13:19: 9000000 INFO @ Tue, 02 Aug 2022 11:13:20: 5000000 INFO @ Tue, 02 Aug 2022 11:13:25: 17000000 INFO @ Tue, 02 Aug 2022 11:13:25: 10000000 INFO @ Tue, 02 Aug 2022 11:13:25: 6000000 INFO @ Tue, 02 Aug 2022 11:13:31: 18000000 INFO @ Tue, 02 Aug 2022 11:13:31: 7000000 INFO @ Tue, 02 Aug 2022 11:13:31: 11000000 INFO @ Tue, 02 Aug 2022 11:13:37: 19000000 INFO @ Tue, 02 Aug 2022 11:13:37: 8000000 INFO @ Tue, 02 Aug 2022 11:13:37: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:13:37: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:13:37: #1 total tags in treatment: 19050492 INFO @ Tue, 02 Aug 2022 11:13:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:13:37: #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 11:13:37: #1 tags after filtering in treatment: 19050492 INFO @ Tue, 02 Aug 2022 11:13:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:13:37: #1 finished! INFO @ Tue, 02 Aug 2022 11:13:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:13:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:13:38: 12000000 INFO @ Tue, 02 Aug 2022 11:13:39: #2 number of paired peaks: 204 WARNING @ Tue, 02 Aug 2022 11:13:39: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 02 Aug 2022 11:13:39: start model_add_line... INFO @ Tue, 02 Aug 2022 11:13:39: start X-correlation... INFO @ Tue, 02 Aug 2022 11:13:39: end of X-cor INFO @ Tue, 02 Aug 2022 11:13:39: #2 finished! INFO @ Tue, 02 Aug 2022 11:13:39: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 11:13:39: #2 alternative fragment length(s) may be 2,62,64,68 bps INFO @ Tue, 02 Aug 2022 11:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.05_model.r WARNING @ Tue, 02 Aug 2022 11:13:39: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:13:39: #2 You may need to consider one of the other alternative d(s): 2,62,64,68 WARNING @ Tue, 02 Aug 2022 11:13:39: #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 11:13:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:13:43: 9000000 INFO @ Tue, 02 Aug 2022 11:13:44: 13000000 INFO @ Tue, 02 Aug 2022 11:13:49: 10000000 INFO @ Tue, 02 Aug 2022 11:13:51: 14000000 INFO @ Tue, 02 Aug 2022 11:13:54: 11000000 INFO @ Tue, 02 Aug 2022 11:13:57: 15000000 INFO @ Tue, 02 Aug 2022 11:14:00: 12000000 INFO @ Tue, 02 Aug 2022 11:14:03: 16000000 INFO @ Tue, 02 Aug 2022 11:14:06: 13000000 INFO @ Tue, 02 Aug 2022 11:14:09: 17000000 INFO @ Tue, 02 Aug 2022 11:14:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:14:11: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:14:16: 18000000 INFO @ Tue, 02 Aug 2022 11:14:17: 15000000 INFO @ Tue, 02 Aug 2022 11:14:22: 19000000 INFO @ Tue, 02 Aug 2022 11:14:22: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:14:22: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:14:22: #1 total tags in treatment: 19050492 INFO @ Tue, 02 Aug 2022 11:14:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:14:22: #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 11:14:23: 16000000 INFO @ Tue, 02 Aug 2022 11:14:23: #1 tags after filtering in treatment: 19050492 INFO @ Tue, 02 Aug 2022 11:14:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:14:23: #1 finished! INFO @ Tue, 02 Aug 2022 11:14:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:14:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:14:24: #2 number of paired peaks: 204 WARNING @ Tue, 02 Aug 2022 11:14:24: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 02 Aug 2022 11:14:24: start model_add_line... INFO @ Tue, 02 Aug 2022 11:14:24: start X-correlation... INFO @ Tue, 02 Aug 2022 11:14:24: end of X-cor INFO @ Tue, 02 Aug 2022 11:14:24: #2 finished! INFO @ Tue, 02 Aug 2022 11:14:24: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 11:14:24: #2 alternative fragment length(s) may be 2,62,64,68 bps INFO @ Tue, 02 Aug 2022 11:14:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.10_model.r WARNING @ Tue, 02 Aug 2022 11:14:24: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:14:24: #2 You may need to consider one of the other alternative d(s): 2,62,64,68 WARNING @ Tue, 02 Aug 2022 11:14:24: #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 11:14:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:14:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.05_summits.bed INFO @ Tue, 02 Aug 2022 11:14:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (739 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:14:28: 17000000 INFO @ Tue, 02 Aug 2022 11:14:33: 18000000 INFO @ Tue, 02 Aug 2022 11:14:38: 19000000 INFO @ Tue, 02 Aug 2022 11:14:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:14:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:14:39: #1 total tags in treatment: 19050492 INFO @ Tue, 02 Aug 2022 11:14:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:14:39: #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 11:14:39: #1 tags after filtering in treatment: 19050492 INFO @ Tue, 02 Aug 2022 11:14:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:14:39: #1 finished! INFO @ Tue, 02 Aug 2022 11:14:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:14:40: #2 number of paired peaks: 204 WARNING @ Tue, 02 Aug 2022 11:14:40: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 02 Aug 2022 11:14:40: start model_add_line... INFO @ Tue, 02 Aug 2022 11:14:40: start X-correlation... INFO @ Tue, 02 Aug 2022 11:14:40: end of X-cor INFO @ Tue, 02 Aug 2022 11:14:40: #2 finished! INFO @ Tue, 02 Aug 2022 11:14:40: #2 predicted fragment length is 68 bps INFO @ Tue, 02 Aug 2022 11:14:40: #2 alternative fragment length(s) may be 2,62,64,68 bps INFO @ Tue, 02 Aug 2022 11:14:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.20_model.r WARNING @ Tue, 02 Aug 2022 11:14:40: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:14:40: #2 You may need to consider one of the other alternative d(s): 2,62,64,68 WARNING @ Tue, 02 Aug 2022 11:14:40: #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 11:14:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:14:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:14:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:15:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:15:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:15:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.10_summits.bed INFO @ Tue, 02 Aug 2022 11:15:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:15:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:15:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:15:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:15:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110362/SRX13110362.20_summits.bed INFO @ Tue, 02 Aug 2022 11:15:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (235 records, 4 fields): 26 millis CompletedMACS2peakCalling