Job ID = 16439685 SRX = SRX13572054 Genome = dm6 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: 00:00:01 Multiseed full-index search: 00:06:29 20406788 reads; of these: 20406788 (100.00%) were unpaired; of these: 805309 (3.95%) aligned 0 times 16460047 (80.66%) aligned exactly 1 time 3141432 (15.39%) aligned >1 times 96.05% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1931245 / 19601479 = 0.0985 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 16:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 16:08:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:08:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:08:52: 1000000 INFO @ Tue, 02 Aug 2022 16:09:02: 2000000 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 16:09:11: 3000000 INFO @ Tue, 02 Aug 2022 16:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 16:09:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:09:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:09:21: 4000000 INFO @ Tue, 02 Aug 2022 16:09:21: 1000000 INFO @ Tue, 02 Aug 2022 16:09:30: 2000000 INFO @ Tue, 02 Aug 2022 16:09:31: 5000000 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 16:09:39: 3000000 INFO @ Tue, 02 Aug 2022 16:09:41: 6000000 INFO @ Tue, 02 Aug 2022 16:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.bam'] # control file = None # effective genome size = 1.20e+08 # 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 16:09:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:09:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:09:48: 4000000 INFO @ Tue, 02 Aug 2022 16:09:50: 1000000 INFO @ Tue, 02 Aug 2022 16:09:50: 7000000 INFO @ Tue, 02 Aug 2022 16:09:57: 5000000 INFO @ Tue, 02 Aug 2022 16:09:59: 2000000 INFO @ Tue, 02 Aug 2022 16:10:00: 8000000 INFO @ Tue, 02 Aug 2022 16:10:06: 6000000 INFO @ Tue, 02 Aug 2022 16:10:07: 3000000 INFO @ Tue, 02 Aug 2022 16:10:10: 9000000 INFO @ Tue, 02 Aug 2022 16:10:15: 7000000 INFO @ Tue, 02 Aug 2022 16:10:17: 4000000 INFO @ Tue, 02 Aug 2022 16:10:20: 10000000 INFO @ Tue, 02 Aug 2022 16:10:25: 8000000 INFO @ Tue, 02 Aug 2022 16:10:27: 5000000 INFO @ Tue, 02 Aug 2022 16:10:30: 11000000 INFO @ Tue, 02 Aug 2022 16:10:35: 9000000 INFO @ Tue, 02 Aug 2022 16:10:37: 6000000 INFO @ Tue, 02 Aug 2022 16:10:40: 12000000 INFO @ Tue, 02 Aug 2022 16:10:45: 10000000 INFO @ Tue, 02 Aug 2022 16:10:46: 7000000 INFO @ Tue, 02 Aug 2022 16:10:50: 13000000 INFO @ Tue, 02 Aug 2022 16:10:54: 11000000 INFO @ Tue, 02 Aug 2022 16:10:56: 8000000 INFO @ Tue, 02 Aug 2022 16:11:00: 14000000 INFO @ Tue, 02 Aug 2022 16:11:04: 12000000 INFO @ Tue, 02 Aug 2022 16:11:06: 9000000 INFO @ Tue, 02 Aug 2022 16:11:10: 15000000 INFO @ Tue, 02 Aug 2022 16:11:13: 13000000 INFO @ Tue, 02 Aug 2022 16:11:15: 10000000 INFO @ Tue, 02 Aug 2022 16:11:20: 16000000 INFO @ Tue, 02 Aug 2022 16:11:23: 14000000 INFO @ Tue, 02 Aug 2022 16:11:25: 11000000 INFO @ Tue, 02 Aug 2022 16:11:29: 17000000 INFO @ Tue, 02 Aug 2022 16:11:34: 15000000 INFO @ Tue, 02 Aug 2022 16:11:34: 12000000 INFO @ Tue, 02 Aug 2022 16:11:36: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:11:36: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:11:36: #1 total tags in treatment: 17670234 INFO @ Tue, 02 Aug 2022 16:11:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:11:36: #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 16:11:37: #1 tags after filtering in treatment: 17670226 INFO @ Tue, 02 Aug 2022 16:11:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:11:37: #1 finished! INFO @ Tue, 02 Aug 2022 16:11:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:11:39: #2 number of paired peaks: 148 WARNING @ Tue, 02 Aug 2022 16:11:39: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 02 Aug 2022 16:11:39: start model_add_line... INFO @ Tue, 02 Aug 2022 16:11:39: start X-correlation... INFO @ Tue, 02 Aug 2022 16:11:39: end of X-cor INFO @ Tue, 02 Aug 2022 16:11:39: #2 finished! INFO @ Tue, 02 Aug 2022 16:11:39: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 16:11:39: #2 alternative fragment length(s) may be 70,86 bps INFO @ Tue, 02 Aug 2022 16:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.05_model.r WARNING @ Tue, 02 Aug 2022 16:11:39: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:11:39: #2 You may need to consider one of the other alternative d(s): 70,86 WARNING @ Tue, 02 Aug 2022 16:11:39: #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 16:11:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:11:44: 13000000 INFO @ Tue, 02 Aug 2022 16:11:44: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:11:53: 14000000 INFO @ Tue, 02 Aug 2022 16:11:54: 17000000 INFO @ Tue, 02 Aug 2022 16:12:00: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:12:00: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:12:00: #1 total tags in treatment: 17670234 INFO @ Tue, 02 Aug 2022 16:12:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:12:00: #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 16:12:01: #1 tags after filtering in treatment: 17670226 INFO @ Tue, 02 Aug 2022 16:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:12:01: #1 finished! INFO @ Tue, 02 Aug 2022 16:12:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:12:03: 15000000 INFO @ Tue, 02 Aug 2022 16:12:03: #2 number of paired peaks: 148 WARNING @ Tue, 02 Aug 2022 16:12:03: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 02 Aug 2022 16:12:03: start model_add_line... INFO @ Tue, 02 Aug 2022 16:12:03: start X-correlation... INFO @ Tue, 02 Aug 2022 16:12:03: end of X-cor INFO @ Tue, 02 Aug 2022 16:12:03: #2 finished! INFO @ Tue, 02 Aug 2022 16:12:03: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 16:12:03: #2 alternative fragment length(s) may be 70,86 bps INFO @ Tue, 02 Aug 2022 16:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.10_model.r WARNING @ Tue, 02 Aug 2022 16:12:03: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:12:03: #2 You may need to consider one of the other alternative d(s): 70,86 WARNING @ Tue, 02 Aug 2022 16:12:03: #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 16:12:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:12:11: 16000000 INFO @ Tue, 02 Aug 2022 16:12:20: 17000000 INFO @ Tue, 02 Aug 2022 16:12:26: #1 tag size is determined as 49 bps INFO @ Tue, 02 Aug 2022 16:12:26: #1 tag size = 49 INFO @ Tue, 02 Aug 2022 16:12:26: #1 total tags in treatment: 17670234 INFO @ Tue, 02 Aug 2022 16:12:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:12:26: #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 16:12:27: #1 tags after filtering in treatment: 17670226 INFO @ Tue, 02 Aug 2022 16:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:12:27: #1 finished! INFO @ Tue, 02 Aug 2022 16:12:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:12:29: #2 number of paired peaks: 148 WARNING @ Tue, 02 Aug 2022 16:12:29: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 02 Aug 2022 16:12:29: start model_add_line... INFO @ Tue, 02 Aug 2022 16:12:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:12:29: start X-correlation... INFO @ Tue, 02 Aug 2022 16:12:29: end of X-cor INFO @ Tue, 02 Aug 2022 16:12:29: #2 finished! INFO @ Tue, 02 Aug 2022 16:12:29: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 16:12:29: #2 alternative fragment length(s) may be 70,86 bps INFO @ Tue, 02 Aug 2022 16:12:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.20_model.r WARNING @ Tue, 02 Aug 2022 16:12:29: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:12:29: #2 You may need to consider one of the other alternative d(s): 70,86 WARNING @ Tue, 02 Aug 2022 16:12:29: #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 16:12:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:12:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:12:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:12:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:12:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:12:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.05_summits.bed INFO @ Tue, 02 Aug 2022 16:12:55: Done! pass1 - making usageList (472 chroms): 3 millis pass2 - checking and writing primary data (1932 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:13:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:13:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:13:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.10_summits.bed INFO @ Tue, 02 Aug 2022 16:13:15: Done! pass1 - making usageList (290 chroms): 3 millis pass2 - checking and writing primary data (946 records, 4 fields): 83 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:13:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:13:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:13:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:13:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13572054/SRX13572054.20_summits.bed INFO @ Tue, 02 Aug 2022 16:13:41: Done! pass1 - making usageList (99 chroms): 2 millis pass2 - checking and writing primary data (373 records, 4 fields): 26 millis CompletedMACS2peakCalling