Job ID = 6529336 SRX = SRX1847043 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: 00:07:10 32091913 reads; of these: 32091913 (100.00%) were unpaired; of these: 1183030 (3.69%) aligned 0 times 27421545 (85.45%) aligned exactly 1 time 3487338 (10.87%) aligned >1 times 96.31% overall alignment rate Time searching: 00:07:10 Overall time: 00:07:10 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 16 files... [bam_rmdupse_core] 11645710 / 30908883 = 0.3768 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.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, 30 Jun 2020 02:35:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:35:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:35:45: 1000000 INFO @ Tue, 30 Jun 2020 02:35:50: 2000000 INFO @ Tue, 30 Jun 2020 02:35:56: 3000000 INFO @ Tue, 30 Jun 2020 02:36:01: 4000000 INFO @ Tue, 30 Jun 2020 02:36:06: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.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, 30 Jun 2020 02:36:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:11: 6000000 INFO @ Tue, 30 Jun 2020 02:36:15: 1000000 INFO @ Tue, 30 Jun 2020 02:36:17: 7000000 INFO @ Tue, 30 Jun 2020 02:36:20: 2000000 INFO @ Tue, 30 Jun 2020 02:36:22: 8000000 INFO @ Tue, 30 Jun 2020 02:36:25: 3000000 INFO @ Tue, 30 Jun 2020 02:36:27: 9000000 INFO @ Tue, 30 Jun 2020 02:36:30: 4000000 INFO @ Tue, 30 Jun 2020 02:36:33: 10000000 INFO @ Tue, 30 Jun 2020 02:36:35: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:36:38: 11000000 INFO @ Tue, 30 Jun 2020 02:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.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, 30 Jun 2020 02:36:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:40: 6000000 INFO @ Tue, 30 Jun 2020 02:36:44: 12000000 INFO @ Tue, 30 Jun 2020 02:36:45: 1000000 INFO @ Tue, 30 Jun 2020 02:36:45: 7000000 INFO @ Tue, 30 Jun 2020 02:36:49: 13000000 INFO @ Tue, 30 Jun 2020 02:36:50: 8000000 INFO @ Tue, 30 Jun 2020 02:36:50: 2000000 INFO @ Tue, 30 Jun 2020 02:36:54: 14000000 INFO @ Tue, 30 Jun 2020 02:36:55: 9000000 INFO @ Tue, 30 Jun 2020 02:36:56: 3000000 INFO @ Tue, 30 Jun 2020 02:36:59: 10000000 INFO @ Tue, 30 Jun 2020 02:37:00: 15000000 INFO @ Tue, 30 Jun 2020 02:37:01: 4000000 INFO @ Tue, 30 Jun 2020 02:37:04: 11000000 INFO @ Tue, 30 Jun 2020 02:37:05: 16000000 INFO @ Tue, 30 Jun 2020 02:37:07: 5000000 INFO @ Tue, 30 Jun 2020 02:37:09: 12000000 INFO @ Tue, 30 Jun 2020 02:37:11: 17000000 INFO @ Tue, 30 Jun 2020 02:37:12: 6000000 INFO @ Tue, 30 Jun 2020 02:37:14: 13000000 INFO @ Tue, 30 Jun 2020 02:37:16: 18000000 INFO @ Tue, 30 Jun 2020 02:37:17: 7000000 INFO @ Tue, 30 Jun 2020 02:37:19: 14000000 INFO @ Tue, 30 Jun 2020 02:37:22: 19000000 INFO @ Tue, 30 Jun 2020 02:37:23: 8000000 INFO @ Tue, 30 Jun 2020 02:37:23: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:37:23: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:37:23: #1 total tags in treatment: 19263173 INFO @ Tue, 30 Jun 2020 02:37:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:37:24: 15000000 INFO @ Tue, 30 Jun 2020 02:37:24: #1 tags after filtering in treatment: 19263171 INFO @ Tue, 30 Jun 2020 02:37:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:25: #2 number of paired peaks: 119 WARNING @ Tue, 30 Jun 2020 02:37:25: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:25: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 02:37:25: #2 alternative fragment length(s) may be 70,84 bps INFO @ Tue, 30 Jun 2020 02:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.05_model.r WARNING @ Tue, 30 Jun 2020 02:37:25: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:25: #2 You may need to consider one of the other alternative d(s): 70,84 WARNING @ Tue, 30 Jun 2020 02:37:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:37:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:28: 9000000 INFO @ Tue, 30 Jun 2020 02:37:29: 16000000 INFO @ Tue, 30 Jun 2020 02:37:33: 10000000 INFO @ Tue, 30 Jun 2020 02:37:34: 17000000 INFO @ Tue, 30 Jun 2020 02:37:39: 18000000 INFO @ Tue, 30 Jun 2020 02:37:39: 11000000 INFO @ Tue, 30 Jun 2020 02:37:44: 19000000 INFO @ Tue, 30 Jun 2020 02:37:44: 12000000 INFO @ Tue, 30 Jun 2020 02:37:45: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:37:45: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:37:45: #1 total tags in treatment: 19263173 INFO @ Tue, 30 Jun 2020 02:37:45: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:37:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:37:46: #1 tags after filtering in treatment: 19263171 INFO @ Tue, 30 Jun 2020 02:37:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:37:46: #1 finished! INFO @ Tue, 30 Jun 2020 02:37:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:37:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:37:47: #2 number of paired peaks: 119 WARNING @ Tue, 30 Jun 2020 02:37:47: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 30 Jun 2020 02:37:47: start model_add_line... INFO @ Tue, 30 Jun 2020 02:37:47: start X-correlation... INFO @ Tue, 30 Jun 2020 02:37:47: end of X-cor INFO @ Tue, 30 Jun 2020 02:37:47: #2 finished! INFO @ Tue, 30 Jun 2020 02:37:47: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 02:37:47: #2 alternative fragment length(s) may be 70,84 bps INFO @ Tue, 30 Jun 2020 02:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.10_model.r WARNING @ Tue, 30 Jun 2020 02:37:47: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:37:47: #2 You may need to consider one of the other alternative d(s): 70,84 WARNING @ Tue, 30 Jun 2020 02:37:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:37:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:37:50: 13000000 INFO @ Tue, 30 Jun 2020 02:37:55: 14000000 INFO @ Tue, 30 Jun 2020 02:37:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:00: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:38:06: 16000000 INFO @ Tue, 30 Jun 2020 02:38:11: 17000000 INFO @ Tue, 30 Jun 2020 02:38:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.05_summits.bed INFO @ Tue, 30 Jun 2020 02:38:16: Done! INFO @ Tue, 30 Jun 2020 02:38:17: 18000000 pass1 - making usageList (115 chroms): 2 millis pass2 - checking and writing primary data (6816 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:38:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:38:22: 19000000 INFO @ Tue, 30 Jun 2020 02:38:24: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:38:24: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:38:24: #1 total tags in treatment: 19263173 INFO @ Tue, 30 Jun 2020 02:38:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:38:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:38:24: #1 tags after filtering in treatment: 19263171 INFO @ Tue, 30 Jun 2020 02:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:38:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:38:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:38:25: #2 number of paired peaks: 119 WARNING @ Tue, 30 Jun 2020 02:38:25: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Tue, 30 Jun 2020 02:38:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:38:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:38:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:38:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:38:26: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 02:38:26: #2 alternative fragment length(s) may be 70,84 bps INFO @ Tue, 30 Jun 2020 02:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.20_model.r WARNING @ Tue, 30 Jun 2020 02:38:26: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:38:26: #2 You may need to consider one of the other alternative d(s): 70,84 WARNING @ Tue, 30 Jun 2020 02:38:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:38:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:38:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:38:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:38:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.10_summits.bed INFO @ Tue, 30 Jun 2020 02:38:37: Done! pass1 - making usageList (88 chroms): 1 millis pass2 - checking and writing primary data (4097 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:39:02: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:39:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:39:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:39:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847043/SRX1847043.20_summits.bed INFO @ Tue, 30 Jun 2020 02:39:21: Done! pass1 - making usageList (54 chroms): 0 millis pass2 - checking and writing primary data (1054 records, 4 fields): 4 millis CompletedMACS2peakCalling