Job ID = 14168989 SRX = SRX8688981 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: 00:07:58 21135837 reads; of these: 21135837 (100.00%) were unpaired; of these: 733018 (3.47%) aligned 0 times 13591845 (64.31%) aligned exactly 1 time 6810974 (32.22%) aligned >1 times 96.53% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 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] 3149576 / 20402819 = 0.1544 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 22:52:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.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 22:52:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:52:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:52:36: 1000000 INFO @ Fri, 10 Dec 2021 22:52:43: 2000000 INFO @ Fri, 10 Dec 2021 22:52:50: 3000000 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 22:52:57: 4000000 INFO @ Fri, 10 Dec 2021 22:52:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.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 22:52:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:52:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:53:05: 5000000 INFO @ Fri, 10 Dec 2021 22:53:06: 1000000 INFO @ Fri, 10 Dec 2021 22:53:12: 6000000 INFO @ Fri, 10 Dec 2021 22:53:13: 2000000 INFO @ Fri, 10 Dec 2021 22:53:19: 3000000 INFO @ Fri, 10 Dec 2021 22:53:19: 7000000 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 22:53:26: 4000000 INFO @ Fri, 10 Dec 2021 22:53:27: 8000000 INFO @ Fri, 10 Dec 2021 22:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.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 22:53:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:53:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:53:32: 5000000 INFO @ Fri, 10 Dec 2021 22:53:35: 9000000 INFO @ Fri, 10 Dec 2021 22:53:36: 1000000 INFO @ Fri, 10 Dec 2021 22:53:39: 6000000 INFO @ Fri, 10 Dec 2021 22:53:42: 10000000 INFO @ Fri, 10 Dec 2021 22:53:44: 2000000 INFO @ Fri, 10 Dec 2021 22:53:46: 7000000 INFO @ Fri, 10 Dec 2021 22:53:51: 11000000 INFO @ Fri, 10 Dec 2021 22:53:52: 3000000 INFO @ Fri, 10 Dec 2021 22:53:53: 8000000 INFO @ Fri, 10 Dec 2021 22:53:59: 12000000 INFO @ Fri, 10 Dec 2021 22:53:59: 9000000 INFO @ Fri, 10 Dec 2021 22:54:00: 4000000 INFO @ Fri, 10 Dec 2021 22:54:06: 10000000 INFO @ Fri, 10 Dec 2021 22:54:07: 13000000 INFO @ Fri, 10 Dec 2021 22:54:08: 5000000 INFO @ Fri, 10 Dec 2021 22:54:14: 11000000 INFO @ Fri, 10 Dec 2021 22:54:15: 14000000 INFO @ Fri, 10 Dec 2021 22:54:15: 6000000 INFO @ Fri, 10 Dec 2021 22:54:21: 12000000 INFO @ Fri, 10 Dec 2021 22:54:23: 7000000 INFO @ Fri, 10 Dec 2021 22:54:24: 15000000 INFO @ Fri, 10 Dec 2021 22:54:28: 13000000 INFO @ Fri, 10 Dec 2021 22:54:31: 8000000 INFO @ Fri, 10 Dec 2021 22:54:32: 16000000 INFO @ Fri, 10 Dec 2021 22:54:35: 14000000 INFO @ Fri, 10 Dec 2021 22:54:39: 9000000 INFO @ Fri, 10 Dec 2021 22:54:40: 17000000 INFO @ Fri, 10 Dec 2021 22:54:42: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:54:42: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:54:42: #1 total tags in treatment: 17253243 INFO @ Fri, 10 Dec 2021 22:54:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:54:42: #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 22:54:42: 15000000 INFO @ Fri, 10 Dec 2021 22:54:43: #1 tags after filtering in treatment: 17253242 INFO @ Fri, 10 Dec 2021 22:54:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:54:43: #1 finished! INFO @ Fri, 10 Dec 2021 22:54:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:54:44: #2 number of paired peaks: 453 WARNING @ Fri, 10 Dec 2021 22:54:44: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Fri, 10 Dec 2021 22:54:44: start model_add_line... INFO @ Fri, 10 Dec 2021 22:54:44: start X-correlation... INFO @ Fri, 10 Dec 2021 22:54:44: end of X-cor INFO @ Fri, 10 Dec 2021 22:54:44: #2 finished! INFO @ Fri, 10 Dec 2021 22:54:44: #2 predicted fragment length is 60 bps INFO @ Fri, 10 Dec 2021 22:54:44: #2 alternative fragment length(s) may be 4,60 bps INFO @ Fri, 10 Dec 2021 22:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.05_model.r WARNING @ Fri, 10 Dec 2021 22:54:44: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:54:44: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Fri, 10 Dec 2021 22:54:44: #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 22:54:44: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:54:46: 10000000 INFO @ Fri, 10 Dec 2021 22:54:49: 16000000 INFO @ Fri, 10 Dec 2021 22:54:54: 11000000 INFO @ Fri, 10 Dec 2021 22:54:57: 17000000 INFO @ Fri, 10 Dec 2021 22:54:59: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:54:59: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:54:59: #1 total tags in treatment: 17253243 INFO @ Fri, 10 Dec 2021 22:54:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:54:59: #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 22:55:00: #1 tags after filtering in treatment: 17253242 INFO @ Fri, 10 Dec 2021 22:55:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:55:00: #1 finished! INFO @ Fri, 10 Dec 2021 22:55:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:55:02: #2 number of paired peaks: 453 WARNING @ Fri, 10 Dec 2021 22:55:02: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Fri, 10 Dec 2021 22:55:02: start model_add_line... INFO @ Fri, 10 Dec 2021 22:55:02: start X-correlation... INFO @ Fri, 10 Dec 2021 22:55:02: end of X-cor INFO @ Fri, 10 Dec 2021 22:55:02: #2 finished! INFO @ Fri, 10 Dec 2021 22:55:02: #2 predicted fragment length is 60 bps INFO @ Fri, 10 Dec 2021 22:55:02: #2 alternative fragment length(s) may be 4,60 bps INFO @ Fri, 10 Dec 2021 22:55:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.10_model.r WARNING @ Fri, 10 Dec 2021 22:55:02: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:55:02: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Fri, 10 Dec 2021 22:55:02: #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 22:55:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:55:02: 12000000 INFO @ Fri, 10 Dec 2021 22:55:09: 13000000 INFO @ Fri, 10 Dec 2021 22:55:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:55:17: 14000000 INFO @ Fri, 10 Dec 2021 22:55:25: 15000000 INFO @ Fri, 10 Dec 2021 22:55:33: 16000000 INFO @ Fri, 10 Dec 2021 22:55:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:55:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:55:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:55:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.05_summits.bed INFO @ Fri, 10 Dec 2021 22:55:37: Done! pass1 - making usageList (920 chroms): 20 millis pass2 - checking and writing primary data (4266 records, 4 fields): 102 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:55:40: 17000000 INFO @ Fri, 10 Dec 2021 22:55:43: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:55:43: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:55:43: #1 total tags in treatment: 17253243 INFO @ Fri, 10 Dec 2021 22:55:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:55:43: #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 22:55:43: #1 tags after filtering in treatment: 17253242 INFO @ Fri, 10 Dec 2021 22:55:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 22:55:43: #1 finished! INFO @ Fri, 10 Dec 2021 22:55:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:55:45: #2 number of paired peaks: 453 WARNING @ Fri, 10 Dec 2021 22:55:45: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Fri, 10 Dec 2021 22:55:45: start model_add_line... INFO @ Fri, 10 Dec 2021 22:55:45: start X-correlation... INFO @ Fri, 10 Dec 2021 22:55:45: end of X-cor INFO @ Fri, 10 Dec 2021 22:55:45: #2 finished! INFO @ Fri, 10 Dec 2021 22:55:45: #2 predicted fragment length is 60 bps INFO @ Fri, 10 Dec 2021 22:55:45: #2 alternative fragment length(s) may be 4,60 bps INFO @ Fri, 10 Dec 2021 22:55:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.20_model.r WARNING @ Fri, 10 Dec 2021 22:55:45: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 22:55:45: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Fri, 10 Dec 2021 22:55:45: #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 22:55:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:55:45: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:55:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:55:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:55:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.10_summits.bed INFO @ Fri, 10 Dec 2021 22:55:52: Done! pass1 - making usageList (608 chroms): 1 millis pass2 - checking and writing primary data (1890 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:56:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:56:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:56:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:56:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688981/SRX8688981.20_summits.bed INFO @ Fri, 10 Dec 2021 22:56:36: Done! pass1 - making usageList (335 chroms): 1 millis pass2 - checking and writing primary data (744 records, 4 fields): 22 millis CompletedMACS2peakCalling