Job ID = 14167539 SRX = SRX4712940 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: 00:00:00 Multiseed full-index search: 00:03:28 13123785 reads; of these: 13123785 (100.00%) were unpaired; of these: 602224 (4.59%) aligned 0 times 9439294 (71.93%) aligned exactly 1 time 3082267 (23.49%) aligned >1 times 95.41% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 1465443 / 12521561 = 0.1170 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:40:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.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 @ Fri, 10 Dec 2021 12:40:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:40:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:40:34: 1000000 INFO @ Fri, 10 Dec 2021 12:40:40: 2000000 INFO @ Fri, 10 Dec 2021 12:40:45: 3000000 INFO @ Fri, 10 Dec 2021 12:40:50: 4000000 INFO @ Fri, 10 Dec 2021 12:40:55: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:40:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.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 @ Fri, 10 Dec 2021 12:40:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:40:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:41:00: 6000000 INFO @ Fri, 10 Dec 2021 12:41:05: 1000000 INFO @ Fri, 10 Dec 2021 12:41:06: 7000000 INFO @ Fri, 10 Dec 2021 12:41:11: 2000000 INFO @ Fri, 10 Dec 2021 12:41:12: 8000000 INFO @ Fri, 10 Dec 2021 12:41:17: 3000000 INFO @ Fri, 10 Dec 2021 12:41:18: 9000000 INFO @ Fri, 10 Dec 2021 12:41:22: 4000000 INFO @ Fri, 10 Dec 2021 12:41:24: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:41:28: 5000000 INFO @ Fri, 10 Dec 2021 12:41:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.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 @ Fri, 10 Dec 2021 12:41:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:41:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:41:30: 11000000 INFO @ Fri, 10 Dec 2021 12:41:30: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:41:30: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:41:30: #1 total tags in treatment: 11056118 INFO @ Fri, 10 Dec 2021 12:41:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:41:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:41:31: #1 tags after filtering in treatment: 11056109 INFO @ Fri, 10 Dec 2021 12:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:41:31: #1 finished! INFO @ Fri, 10 Dec 2021 12:41:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:41:31: #2 number of paired peaks: 334 WARNING @ Fri, 10 Dec 2021 12:41:31: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Fri, 10 Dec 2021 12:41:31: start model_add_line... INFO @ Fri, 10 Dec 2021 12:41:31: start X-correlation... INFO @ Fri, 10 Dec 2021 12:41:31: end of X-cor INFO @ Fri, 10 Dec 2021 12:41:31: #2 finished! INFO @ Fri, 10 Dec 2021 12:41:31: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 12:41:31: #2 alternative fragment length(s) may be 57 bps INFO @ Fri, 10 Dec 2021 12:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.05_model.r WARNING @ Fri, 10 Dec 2021 12:41:31: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:41:31: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Fri, 10 Dec 2021 12:41:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:41:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:41:34: 6000000 INFO @ Fri, 10 Dec 2021 12:41:35: 1000000 INFO @ Fri, 10 Dec 2021 12:41:40: 7000000 INFO @ Fri, 10 Dec 2021 12:41:41: 2000000 INFO @ Fri, 10 Dec 2021 12:41:45: 8000000 INFO @ Fri, 10 Dec 2021 12:41:47: 3000000 INFO @ Fri, 10 Dec 2021 12:41:52: 9000000 INFO @ Fri, 10 Dec 2021 12:41:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:41:53: 4000000 INFO @ Fri, 10 Dec 2021 12:41:57: 10000000 INFO @ Fri, 10 Dec 2021 12:42:00: 5000000 INFO @ Fri, 10 Dec 2021 12:42:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:42:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:42:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.05_summits.bed INFO @ Fri, 10 Dec 2021 12:42:03: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (2662 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:42:03: 11000000 INFO @ Fri, 10 Dec 2021 12:42:04: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:42:04: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:42:04: #1 total tags in treatment: 11056118 INFO @ Fri, 10 Dec 2021 12:42:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:42:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:42:04: #1 tags after filtering in treatment: 11056109 INFO @ Fri, 10 Dec 2021 12:42:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:42:04: #1 finished! INFO @ Fri, 10 Dec 2021 12:42:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:42:05: #2 number of paired peaks: 334 WARNING @ Fri, 10 Dec 2021 12:42:05: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Fri, 10 Dec 2021 12:42:05: start model_add_line... INFO @ Fri, 10 Dec 2021 12:42:05: start X-correlation... INFO @ Fri, 10 Dec 2021 12:42:05: end of X-cor INFO @ Fri, 10 Dec 2021 12:42:05: #2 finished! INFO @ Fri, 10 Dec 2021 12:42:05: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 12:42:05: #2 alternative fragment length(s) may be 57 bps INFO @ Fri, 10 Dec 2021 12:42:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.10_model.r WARNING @ Fri, 10 Dec 2021 12:42:05: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:42:05: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Fri, 10 Dec 2021 12:42:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:42:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:42:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:42:05: 6000000 INFO @ Fri, 10 Dec 2021 12:42:11: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:42:16: 8000000 INFO @ Fri, 10 Dec 2021 12:42:22: 9000000 INFO @ Fri, 10 Dec 2021 12:42:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:42:28: 10000000 INFO @ Fri, 10 Dec 2021 12:42:33: 11000000 INFO @ Fri, 10 Dec 2021 12:42:33: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 12:42:33: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 12:42:33: #1 total tags in treatment: 11056118 INFO @ Fri, 10 Dec 2021 12:42:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:42:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:42:34: #1 tags after filtering in treatment: 11056109 INFO @ Fri, 10 Dec 2021 12:42:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:42:34: #1 finished! INFO @ Fri, 10 Dec 2021 12:42:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:42:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:42:35: #2 number of paired peaks: 334 WARNING @ Fri, 10 Dec 2021 12:42:35: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Fri, 10 Dec 2021 12:42:35: start model_add_line... INFO @ Fri, 10 Dec 2021 12:42:35: start X-correlation... INFO @ Fri, 10 Dec 2021 12:42:35: end of X-cor INFO @ Fri, 10 Dec 2021 12:42:35: #2 finished! INFO @ Fri, 10 Dec 2021 12:42:35: #2 predicted fragment length is 57 bps INFO @ Fri, 10 Dec 2021 12:42:35: #2 alternative fragment length(s) may be 57 bps INFO @ Fri, 10 Dec 2021 12:42:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.20_model.r WARNING @ Fri, 10 Dec 2021 12:42:35: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:42:35: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Fri, 10 Dec 2021 12:42:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:42:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:42:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:42:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:42:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.10_summits.bed INFO @ Fri, 10 Dec 2021 12:42:37: Done! pass1 - making usageList (314 chroms): 1 millis pass2 - checking and writing primary data (852 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:42:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712940/SRX4712940.20_summits.bed INFO @ Fri, 10 Dec 2021 12:43:09: Done! pass1 - making usageList (151 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 6 millis CompletedMACS2peakCalling