Job ID = 16436147 SRX = SRX13110349 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: 00:06:21 20522787 reads; of these: 20522787 (100.00%) were unpaired; of these: 2291302 (11.16%) aligned 0 times 15213342 (74.13%) aligned exactly 1 time 3018143 (14.71%) aligned >1 times 88.84% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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] 2249212 / 18231485 = 0.1234 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 11:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.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 11:10:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:10:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:10:55: 1000000 INFO @ Tue, 02 Aug 2022 11:11:01: 2000000 INFO @ Tue, 02 Aug 2022 11:11:07: 3000000 INFO @ Tue, 02 Aug 2022 11:11:13: 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 11:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.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 11:11:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:11:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:11:19: 5000000 INFO @ Tue, 02 Aug 2022 11:11:25: 6000000 INFO @ Tue, 02 Aug 2022 11:11:27: 1000000 INFO @ Tue, 02 Aug 2022 11:11:32: 7000000 INFO @ Tue, 02 Aug 2022 11:11:35: 2000000 INFO @ Tue, 02 Aug 2022 11:11:38: 8000000 INFO @ Tue, 02 Aug 2022 11:11:43: 3000000 INFO @ Tue, 02 Aug 2022 11:11:44: 9000000 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 11:11:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.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 11:11:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:11:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:11:51: 10000000 INFO @ Tue, 02 Aug 2022 11:11:51: 4000000 INFO @ Tue, 02 Aug 2022 11:11:57: 1000000 INFO @ Tue, 02 Aug 2022 11:11:57: 11000000 INFO @ Tue, 02 Aug 2022 11:12:00: 5000000 INFO @ Tue, 02 Aug 2022 11:12:04: 2000000 INFO @ Tue, 02 Aug 2022 11:12:04: 12000000 INFO @ Tue, 02 Aug 2022 11:12:08: 6000000 INFO @ Tue, 02 Aug 2022 11:12:12: 3000000 INFO @ Tue, 02 Aug 2022 11:12:12: 13000000 INFO @ Tue, 02 Aug 2022 11:12:17: 7000000 INFO @ Tue, 02 Aug 2022 11:12:19: 14000000 INFO @ Tue, 02 Aug 2022 11:12:19: 4000000 INFO @ Tue, 02 Aug 2022 11:12:26: 8000000 INFO @ Tue, 02 Aug 2022 11:12:27: 15000000 INFO @ Tue, 02 Aug 2022 11:12:27: 5000000 INFO @ Tue, 02 Aug 2022 11:12:34: 9000000 INFO @ Tue, 02 Aug 2022 11:12:34: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:12:34: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:12:34: #1 total tags in treatment: 15982273 INFO @ Tue, 02 Aug 2022 11:12:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:12:34: #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 11:12:34: #1 tags after filtering in treatment: 15982273 INFO @ Tue, 02 Aug 2022 11:12:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:12:34: #1 finished! INFO @ Tue, 02 Aug 2022 11:12:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:12:34: 6000000 INFO @ Tue, 02 Aug 2022 11:12:35: #2 number of paired peaks: 312 WARNING @ Tue, 02 Aug 2022 11:12:35: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Tue, 02 Aug 2022 11:12:35: start model_add_line... INFO @ Tue, 02 Aug 2022 11:12:36: start X-correlation... INFO @ Tue, 02 Aug 2022 11:12:36: end of X-cor INFO @ Tue, 02 Aug 2022 11:12:36: #2 finished! INFO @ Tue, 02 Aug 2022 11:12:36: #2 predicted fragment length is 110 bps INFO @ Tue, 02 Aug 2022 11:12:36: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 02 Aug 2022 11:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.05_model.r WARNING @ Tue, 02 Aug 2022 11:12:36: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:12:36: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 02 Aug 2022 11:12:36: #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 11:12:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:12:42: 10000000 INFO @ Tue, 02 Aug 2022 11:12:42: 7000000 INFO @ Tue, 02 Aug 2022 11:12:50: 8000000 INFO @ Tue, 02 Aug 2022 11:12:50: 11000000 INFO @ Tue, 02 Aug 2022 11:12:57: 9000000 INFO @ Tue, 02 Aug 2022 11:12:58: 12000000 INFO @ Tue, 02 Aug 2022 11:13:05: 10000000 INFO @ Tue, 02 Aug 2022 11:13:05: 13000000 INFO @ Tue, 02 Aug 2022 11:13:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:13:12: 11000000 INFO @ Tue, 02 Aug 2022 11:13:13: 14000000 INFO @ Tue, 02 Aug 2022 11:13:19: 12000000 INFO @ Tue, 02 Aug 2022 11:13:21: 15000000 INFO @ Tue, 02 Aug 2022 11:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.05_summits.bed INFO @ Tue, 02 Aug 2022 11:13:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5321 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:13:26: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:13:28: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:13:28: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:13:28: #1 total tags in treatment: 15982273 INFO @ Tue, 02 Aug 2022 11:13:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:13:28: #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 11:13:29: #1 tags after filtering in treatment: 15982273 INFO @ Tue, 02 Aug 2022 11:13:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:13:29: #1 finished! INFO @ Tue, 02 Aug 2022 11:13:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:13:30: #2 number of paired peaks: 312 WARNING @ Tue, 02 Aug 2022 11:13:30: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Tue, 02 Aug 2022 11:13:30: start model_add_line... INFO @ Tue, 02 Aug 2022 11:13:30: start X-correlation... INFO @ Tue, 02 Aug 2022 11:13:30: end of X-cor INFO @ Tue, 02 Aug 2022 11:13:30: #2 finished! INFO @ Tue, 02 Aug 2022 11:13:30: #2 predicted fragment length is 110 bps INFO @ Tue, 02 Aug 2022 11:13:30: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 02 Aug 2022 11:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.10_model.r WARNING @ Tue, 02 Aug 2022 11:13:30: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:13:30: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 02 Aug 2022 11:13:30: #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 11:13:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:13:32: 14000000 INFO @ Tue, 02 Aug 2022 11:13:38: 15000000 INFO @ Tue, 02 Aug 2022 11:13:44: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:13:44: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:13:44: #1 total tags in treatment: 15982273 INFO @ Tue, 02 Aug 2022 11:13:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:13:44: #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 11:13:44: #1 tags after filtering in treatment: 15982273 INFO @ Tue, 02 Aug 2022 11:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:13:44: #1 finished! INFO @ Tue, 02 Aug 2022 11:13:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:13:46: #2 number of paired peaks: 312 WARNING @ Tue, 02 Aug 2022 11:13:46: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Tue, 02 Aug 2022 11:13:46: start model_add_line... INFO @ Tue, 02 Aug 2022 11:13:46: start X-correlation... INFO @ Tue, 02 Aug 2022 11:13:46: end of X-cor INFO @ Tue, 02 Aug 2022 11:13:46: #2 finished! INFO @ Tue, 02 Aug 2022 11:13:46: #2 predicted fragment length is 110 bps INFO @ Tue, 02 Aug 2022 11:13:46: #2 alternative fragment length(s) may be 110 bps INFO @ Tue, 02 Aug 2022 11:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.20_model.r WARNING @ Tue, 02 Aug 2022 11:13:46: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:13:46: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Tue, 02 Aug 2022 11:13:46: #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 11:13:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:13:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:14:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:14:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:14:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.10_summits.bed INFO @ Tue, 02 Aug 2022 11:14:15: Done! INFO @ Tue, 02 Aug 2022 11:14:15: #3 Call peaks for each chromosome... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2835 records, 4 fields): 110 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110349/SRX13110349.20_summits.bed INFO @ Tue, 02 Aug 2022 11:14:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1344 records, 4 fields): 15 millis CompletedMACS2peakCalling