Job ID = 16439157 SRX = SRX13227902 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: 00:13:35 25039051 reads; of these: 25039051 (100.00%) were unpaired; of these: 1312157 (5.24%) aligned 0 times 14486898 (57.86%) aligned exactly 1 time 9239996 (36.90%) aligned >1 times 94.76% overall alignment rate Time searching: 00:13:35 Overall time: 00:13:35 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14239756 / 23726894 = 0.6002 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 14:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.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 14:59:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:59:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:59:51: 1000000 INFO @ Tue, 02 Aug 2022 14:59:57: 2000000 INFO @ Tue, 02 Aug 2022 15:00:04: 3000000 INFO @ Tue, 02 Aug 2022 15:00:11: 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 15:00:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.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 15:00:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:00:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:00:17: 5000000 INFO @ Tue, 02 Aug 2022 15:00:21: 1000000 INFO @ Tue, 02 Aug 2022 15:00:24: 6000000 INFO @ Tue, 02 Aug 2022 15:00:28: 2000000 INFO @ Tue, 02 Aug 2022 15:00:31: 7000000 INFO @ Tue, 02 Aug 2022 15:00:34: 3000000 INFO @ Tue, 02 Aug 2022 15:00:39: 8000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 15:00:41: 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 15:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.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 15:00:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:00:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:00:46: 9000000 INFO @ Tue, 02 Aug 2022 15:00:47: 5000000 INFO @ Tue, 02 Aug 2022 15:00:50: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:00:50: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:00:50: #1 total tags in treatment: 9487138 INFO @ Tue, 02 Aug 2022 15:00:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:00:50: #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 15:00:51: #1 tags after filtering in treatment: 9487136 INFO @ Tue, 02 Aug 2022 15:00:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:00:51: #1 finished! INFO @ Tue, 02 Aug 2022 15:00:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:00:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:00:52: #2 number of paired peaks: 1259 INFO @ Tue, 02 Aug 2022 15:00:52: start model_add_line... INFO @ Tue, 02 Aug 2022 15:00:52: start X-correlation... INFO @ Tue, 02 Aug 2022 15:00:52: end of X-cor INFO @ Tue, 02 Aug 2022 15:00:52: #2 finished! INFO @ Tue, 02 Aug 2022 15:00:52: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 15:00:52: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 02 Aug 2022 15:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.05_model.r WARNING @ Tue, 02 Aug 2022 15:00:52: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:00:52: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 02 Aug 2022 15:00:52: #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 15:00:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:00:53: 1000000 INFO @ Tue, 02 Aug 2022 15:00:54: 6000000 INFO @ Tue, 02 Aug 2022 15:01:00: 2000000 INFO @ Tue, 02 Aug 2022 15:01:01: 7000000 INFO @ Tue, 02 Aug 2022 15:01:07: 3000000 INFO @ Tue, 02 Aug 2022 15:01:08: 8000000 INFO @ Tue, 02 Aug 2022 15:01:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:01:14: 4000000 INFO @ Tue, 02 Aug 2022 15:01:15: 9000000 INFO @ Tue, 02 Aug 2022 15:01:19: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:01:19: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:01:19: #1 total tags in treatment: 9487138 INFO @ Tue, 02 Aug 2022 15:01:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:01:19: #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 15:01:20: #1 tags after filtering in treatment: 9487136 INFO @ Tue, 02 Aug 2022 15:01:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:01:20: #1 finished! INFO @ Tue, 02 Aug 2022 15:01:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:01:21: #2 number of paired peaks: 1259 INFO @ Tue, 02 Aug 2022 15:01:21: start model_add_line... INFO @ Tue, 02 Aug 2022 15:01:21: 5000000 INFO @ Tue, 02 Aug 2022 15:01:21: start X-correlation... INFO @ Tue, 02 Aug 2022 15:01:21: end of X-cor INFO @ Tue, 02 Aug 2022 15:01:21: #2 finished! INFO @ Tue, 02 Aug 2022 15:01:21: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 15:01:21: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 02 Aug 2022 15:01:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.10_model.r WARNING @ Tue, 02 Aug 2022 15:01:21: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:01:21: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 02 Aug 2022 15:01:21: #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 15:01:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:01:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:01:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:01:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:01:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.05_summits.bed INFO @ Tue, 02 Aug 2022 15:01:22: Done! pass1 - making usageList (837 chroms): 4 millis pass2 - checking and writing primary data (3626 records, 4 fields): 92 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:01:28: 6000000 INFO @ Tue, 02 Aug 2022 15:01:34: 7000000 INFO @ Tue, 02 Aug 2022 15:01:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:01:42: 8000000 INFO @ Tue, 02 Aug 2022 15:01:49: 9000000 INFO @ Tue, 02 Aug 2022 15:01:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:01:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:01:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.10_summits.bed INFO @ Tue, 02 Aug 2022 15:01:49: Done! pass1 - making usageList (650 chroms): 4 millis pass2 - checking and writing primary data (2004 records, 4 fields): 81 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:01:52: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:01:52: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:01:52: #1 total tags in treatment: 9487138 INFO @ Tue, 02 Aug 2022 15:01:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:01:52: #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 15:01:53: #1 tags after filtering in treatment: 9487136 INFO @ Tue, 02 Aug 2022 15:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:01:53: #1 finished! INFO @ Tue, 02 Aug 2022 15:01:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:01:53: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:01:54: #2 number of paired peaks: 1259 INFO @ Tue, 02 Aug 2022 15:01:54: start model_add_line... INFO @ Tue, 02 Aug 2022 15:01:54: start X-correlation... INFO @ Tue, 02 Aug 2022 15:01:54: end of X-cor INFO @ Tue, 02 Aug 2022 15:01:54: #2 finished! INFO @ Tue, 02 Aug 2022 15:01:54: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 15:01:54: #2 alternative fragment length(s) may be 78 bps INFO @ Tue, 02 Aug 2022 15:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.20_model.r WARNING @ Tue, 02 Aug 2022 15:01:54: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:01:54: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Tue, 02 Aug 2022 15:01:54: #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 15:01:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:02:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227902/SRX13227902.20_summits.bed INFO @ Tue, 02 Aug 2022 15:02:22: Done! BigWig に変換しました。 pass1 - making usageList (535 chroms): 1 millis pass2 - checking and writing primary data (1427 records, 4 fields): 77 millis CompletedMACS2peakCalling