Job ID = 16439140 SRX = SRX10031710 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: 00:38:22 86393121 reads; of these: 86393121 (100.00%) were unpaired; of these: 46831651 (54.21%) aligned 0 times 32375374 (37.47%) aligned exactly 1 time 7186096 (8.32%) aligned >1 times 45.79% overall alignment rate Time searching: 00:38:23 Overall time: 00:38:23 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 20 files... [bam_rmdupse_core] 16630784 / 39561470 = 0.4204 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 15:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.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 15:29:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:29:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:29:49: 1000000 INFO @ Tue, 02 Aug 2022 15:30:02: 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 15:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.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 15:30:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:30:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:30:15: 3000000 INFO @ Tue, 02 Aug 2022 15:30:19: 1000000 INFO @ Tue, 02 Aug 2022 15:30:28: 4000000 INFO @ Tue, 02 Aug 2022 15:30:33: 2000000 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 15:30:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.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 15:30:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:30:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:30:40: 5000000 INFO @ Tue, 02 Aug 2022 15:30:47: 3000000 INFO @ Tue, 02 Aug 2022 15:30:50: 1000000 INFO @ Tue, 02 Aug 2022 15:30:53: 6000000 INFO @ Tue, 02 Aug 2022 15:31:02: 4000000 INFO @ Tue, 02 Aug 2022 15:31:04: 2000000 INFO @ Tue, 02 Aug 2022 15:31:06: 7000000 INFO @ Tue, 02 Aug 2022 15:31:16: 5000000 INFO @ Tue, 02 Aug 2022 15:31:18: 3000000 INFO @ Tue, 02 Aug 2022 15:31:18: 8000000 INFO @ Tue, 02 Aug 2022 15:31:30: 6000000 INFO @ Tue, 02 Aug 2022 15:31:31: 9000000 INFO @ Tue, 02 Aug 2022 15:31:31: 4000000 INFO @ Tue, 02 Aug 2022 15:31:43: 10000000 INFO @ Tue, 02 Aug 2022 15:31:43: 7000000 INFO @ Tue, 02 Aug 2022 15:31:44: 5000000 INFO @ Tue, 02 Aug 2022 15:31:55: 11000000 INFO @ Tue, 02 Aug 2022 15:31:57: 8000000 INFO @ Tue, 02 Aug 2022 15:31:58: 6000000 INFO @ Tue, 02 Aug 2022 15:32:08: 12000000 INFO @ Tue, 02 Aug 2022 15:32:10: 9000000 INFO @ Tue, 02 Aug 2022 15:32:12: 7000000 INFO @ Tue, 02 Aug 2022 15:32:21: 13000000 INFO @ Tue, 02 Aug 2022 15:32:24: 10000000 INFO @ Tue, 02 Aug 2022 15:32:25: 8000000 INFO @ Tue, 02 Aug 2022 15:32:34: 14000000 INFO @ Tue, 02 Aug 2022 15:32:38: 11000000 INFO @ Tue, 02 Aug 2022 15:32:39: 9000000 INFO @ Tue, 02 Aug 2022 15:32:47: 15000000 INFO @ Tue, 02 Aug 2022 15:32:51: 12000000 INFO @ Tue, 02 Aug 2022 15:32:53: 10000000 INFO @ Tue, 02 Aug 2022 15:33:00: 16000000 INFO @ Tue, 02 Aug 2022 15:33:05: 13000000 INFO @ Tue, 02 Aug 2022 15:33:07: 11000000 INFO @ Tue, 02 Aug 2022 15:33:13: 17000000 INFO @ Tue, 02 Aug 2022 15:33:18: 14000000 INFO @ Tue, 02 Aug 2022 15:33:20: 12000000 INFO @ Tue, 02 Aug 2022 15:33:26: 18000000 INFO @ Tue, 02 Aug 2022 15:33:31: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:33:34: 13000000 INFO @ Tue, 02 Aug 2022 15:33:39: 19000000 INFO @ Tue, 02 Aug 2022 15:33:44: 16000000 INFO @ Tue, 02 Aug 2022 15:33:48: 14000000 INFO @ Tue, 02 Aug 2022 15:33:52: 20000000 INFO @ Tue, 02 Aug 2022 15:33:57: 17000000 INFO @ Tue, 02 Aug 2022 15:34:01: 15000000 INFO @ Tue, 02 Aug 2022 15:34:05: 21000000 INFO @ Tue, 02 Aug 2022 15:34:11: 18000000 INFO @ Tue, 02 Aug 2022 15:34:14: 16000000 INFO @ Tue, 02 Aug 2022 15:34:19: 22000000 INFO @ Tue, 02 Aug 2022 15:34:25: 19000000 INFO @ Tue, 02 Aug 2022 15:34:27: 17000000 INFO @ Tue, 02 Aug 2022 15:34:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 15:34:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 15:34:32: #1 total tags in treatment: 22930686 INFO @ Tue, 02 Aug 2022 15:34:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:34:32: #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 15:34:33: #1 tags after filtering in treatment: 22930629 INFO @ Tue, 02 Aug 2022 15:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:34:33: #1 finished! INFO @ Tue, 02 Aug 2022 15:34:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:34:35: #2 number of paired peaks: 1126 INFO @ Tue, 02 Aug 2022 15:34:35: start model_add_line... INFO @ Tue, 02 Aug 2022 15:34:36: start X-correlation... INFO @ Tue, 02 Aug 2022 15:34:36: end of X-cor INFO @ Tue, 02 Aug 2022 15:34:36: #2 finished! INFO @ Tue, 02 Aug 2022 15:34:36: #2 predicted fragment length is 30 bps INFO @ Tue, 02 Aug 2022 15:34:36: #2 alternative fragment length(s) may be 30 bps INFO @ Tue, 02 Aug 2022 15:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.05_model.r WARNING @ Tue, 02 Aug 2022 15:34:36: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:34:36: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Tue, 02 Aug 2022 15:34:36: #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 15:34:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:34:39: 20000000 INFO @ Tue, 02 Aug 2022 15:34:41: 18000000 INFO @ Tue, 02 Aug 2022 15:34:52: 21000000 INFO @ Tue, 02 Aug 2022 15:34:54: 19000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:35:06: 22000000 INFO @ Tue, 02 Aug 2022 15:35:07: 20000000 INFO @ Tue, 02 Aug 2022 15:35:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 15:35:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 15:35:20: #1 total tags in treatment: 22930686 INFO @ Tue, 02 Aug 2022 15:35:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:35:20: #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 15:35:20: 21000000 INFO @ Tue, 02 Aug 2022 15:35:21: #1 tags after filtering in treatment: 22930629 INFO @ Tue, 02 Aug 2022 15:35:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:35:21: #1 finished! INFO @ Tue, 02 Aug 2022 15:35:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:35:23: #2 number of paired peaks: 1126 INFO @ Tue, 02 Aug 2022 15:35:23: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:23: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:23: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:23: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:23: #2 predicted fragment length is 30 bps INFO @ Tue, 02 Aug 2022 15:35:23: #2 alternative fragment length(s) may be 30 bps INFO @ Tue, 02 Aug 2022 15:35:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.10_model.r WARNING @ Tue, 02 Aug 2022 15:35:23: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:35:23: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Tue, 02 Aug 2022 15:35:23: #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 15:35:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:35:33: 22000000 INFO @ Tue, 02 Aug 2022 15:35:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:35:46: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 15:35:46: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 15:35:46: #1 total tags in treatment: 22930686 INFO @ Tue, 02 Aug 2022 15:35:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:35:46: #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 15:35:47: #1 tags after filtering in treatment: 22930629 INFO @ Tue, 02 Aug 2022 15:35:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:35:47: #1 finished! INFO @ Tue, 02 Aug 2022 15:35:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:35:49: #2 number of paired peaks: 1126 INFO @ Tue, 02 Aug 2022 15:35:49: start model_add_line... INFO @ Tue, 02 Aug 2022 15:35:50: start X-correlation... INFO @ Tue, 02 Aug 2022 15:35:50: end of X-cor INFO @ Tue, 02 Aug 2022 15:35:50: #2 finished! INFO @ Tue, 02 Aug 2022 15:35:50: #2 predicted fragment length is 30 bps INFO @ Tue, 02 Aug 2022 15:35:50: #2 alternative fragment length(s) may be 30 bps INFO @ Tue, 02 Aug 2022 15:35:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.20_model.r WARNING @ Tue, 02 Aug 2022 15:35:50: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:35:50: #2 You may need to consider one of the other alternative d(s): 30 WARNING @ Tue, 02 Aug 2022 15:35:50: #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 15:35:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.05_summits.bed INFO @ Tue, 02 Aug 2022 15:36:11: Done! pass1 - making usageList (626 chroms): 7 millis pass2 - checking and writing primary data (16163 records, 4 fields): 83 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:36:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:36:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.10_summits.bed INFO @ Tue, 02 Aug 2022 15:36:50: Done! pass1 - making usageList (407 chroms): 15 millis pass2 - checking and writing primary data (10014 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031710/SRX10031710.20_summits.bed INFO @ Tue, 02 Aug 2022 15:37:18: Done! pass1 - making usageList (154 chroms): 3 millis pass2 - checking and writing primary data (4592 records, 4 fields): 49 millis CompletedMACS2peakCalling