Job ID = 6529735 SRX = SRX4664654 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: 00:09:28 31300231 reads; of these: 31300231 (100.00%) were unpaired; of these: 913836 (2.92%) aligned 0 times 20662827 (66.01%) aligned exactly 1 time 9723568 (31.07%) aligned >1 times 97.08% overall alignment rate Time searching: 00:09:28 Overall time: 00:09:28 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 16 files... [bam_rmdupse_core] 5846477 / 30386395 = 0.1924 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 02:45:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.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 02:45:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:50: 1000000 INFO @ Tue, 30 Jun 2020 02:45:56: 2000000 INFO @ Tue, 30 Jun 2020 02:46:03: 3000000 INFO @ Tue, 30 Jun 2020 02:46:10: 4000000 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 02:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.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 02:46:12: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:12: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:16: 5000000 INFO @ Tue, 30 Jun 2020 02:46:18: 1000000 INFO @ Tue, 30 Jun 2020 02:46:22: 6000000 INFO @ Tue, 30 Jun 2020 02:46:24: 2000000 INFO @ Tue, 30 Jun 2020 02:46:29: 7000000 INFO @ Tue, 30 Jun 2020 02:46:29: 3000000 INFO @ Tue, 30 Jun 2020 02:46:34: 4000000 INFO @ Tue, 30 Jun 2020 02:46:35: 8000000 INFO @ Tue, 30 Jun 2020 02:46:40: 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 02:46:42: 9000000 INFO @ Tue, 30 Jun 2020 02:46:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.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 02:46:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:45: 6000000 INFO @ Tue, 30 Jun 2020 02:46:48: 1000000 INFO @ Tue, 30 Jun 2020 02:46:48: 10000000 INFO @ Tue, 30 Jun 2020 02:46:51: 7000000 INFO @ Tue, 30 Jun 2020 02:46:54: 2000000 INFO @ Tue, 30 Jun 2020 02:46:55: 11000000 INFO @ Tue, 30 Jun 2020 02:46:56: 8000000 INFO @ Tue, 30 Jun 2020 02:46:59: 3000000 INFO @ Tue, 30 Jun 2020 02:47:02: 12000000 INFO @ Tue, 30 Jun 2020 02:47:02: 9000000 INFO @ Tue, 30 Jun 2020 02:47:05: 4000000 INFO @ Tue, 30 Jun 2020 02:47:07: 10000000 INFO @ Tue, 30 Jun 2020 02:47:08: 13000000 INFO @ Tue, 30 Jun 2020 02:47:10: 5000000 INFO @ Tue, 30 Jun 2020 02:47:13: 11000000 INFO @ Tue, 30 Jun 2020 02:47:15: 14000000 INFO @ Tue, 30 Jun 2020 02:47:16: 6000000 INFO @ Tue, 30 Jun 2020 02:47:19: 12000000 INFO @ Tue, 30 Jun 2020 02:47:21: 7000000 INFO @ Tue, 30 Jun 2020 02:47:22: 15000000 INFO @ Tue, 30 Jun 2020 02:47:24: 13000000 INFO @ Tue, 30 Jun 2020 02:47:27: 8000000 INFO @ Tue, 30 Jun 2020 02:47:28: 16000000 INFO @ Tue, 30 Jun 2020 02:47:30: 14000000 INFO @ Tue, 30 Jun 2020 02:47:32: 9000000 INFO @ Tue, 30 Jun 2020 02:47:34: 17000000 INFO @ Tue, 30 Jun 2020 02:47:36: 15000000 INFO @ Tue, 30 Jun 2020 02:47:38: 10000000 INFO @ Tue, 30 Jun 2020 02:47:40: 18000000 INFO @ Tue, 30 Jun 2020 02:47:42: 16000000 INFO @ Tue, 30 Jun 2020 02:47:44: 11000000 INFO @ Tue, 30 Jun 2020 02:47:46: 19000000 INFO @ Tue, 30 Jun 2020 02:47:47: 17000000 INFO @ Tue, 30 Jun 2020 02:47:50: 12000000 INFO @ Tue, 30 Jun 2020 02:47:52: 20000000 INFO @ Tue, 30 Jun 2020 02:47:53: 18000000 INFO @ Tue, 30 Jun 2020 02:47:55: 13000000 INFO @ Tue, 30 Jun 2020 02:47:58: 21000000 INFO @ Tue, 30 Jun 2020 02:47:58: 19000000 INFO @ Tue, 30 Jun 2020 02:48:01: 14000000 INFO @ Tue, 30 Jun 2020 02:48:04: 22000000 INFO @ Tue, 30 Jun 2020 02:48:04: 20000000 INFO @ Tue, 30 Jun 2020 02:48:07: 15000000 INFO @ Tue, 30 Jun 2020 02:48:09: 23000000 INFO @ Tue, 30 Jun 2020 02:48:11: 21000000 INFO @ Tue, 30 Jun 2020 02:48:13: 16000000 INFO @ Tue, 30 Jun 2020 02:48:15: 24000000 INFO @ Tue, 30 Jun 2020 02:48:16: 22000000 INFO @ Tue, 30 Jun 2020 02:48:18: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:48:18: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:48:18: #1 total tags in treatment: 24539918 INFO @ Tue, 30 Jun 2020 02:48:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:18: #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 02:48:18: 17000000 INFO @ Tue, 30 Jun 2020 02:48:19: #1 tags after filtering in treatment: 24539859 INFO @ Tue, 30 Jun 2020 02:48:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:19: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:21: #2 number of paired peaks: 890 WARNING @ Tue, 30 Jun 2020 02:48:21: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:21: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:21: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:21: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:21: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:48:21: #2 alternative fragment length(s) may be 1,48 bps INFO @ Tue, 30 Jun 2020 02:48:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.05_model.r WARNING @ Tue, 30 Jun 2020 02:48:21: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:21: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Tue, 30 Jun 2020 02:48:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:48:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:22: 23000000 INFO @ Tue, 30 Jun 2020 02:48:24: 18000000 INFO @ Tue, 30 Jun 2020 02:48:28: 24000000 INFO @ Tue, 30 Jun 2020 02:48:30: 19000000 INFO @ Tue, 30 Jun 2020 02:48:31: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:48:31: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:48:31: #1 total tags in treatment: 24539918 INFO @ Tue, 30 Jun 2020 02:48:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:31: #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 02:48:32: #1 tags after filtering in treatment: 24539859 INFO @ Tue, 30 Jun 2020 02:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:34: #2 number of paired peaks: 890 WARNING @ Tue, 30 Jun 2020 02:48:34: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:34: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:34: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:34: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:34: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:34: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:48:34: #2 alternative fragment length(s) may be 1,48 bps INFO @ Tue, 30 Jun 2020 02:48:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.10_model.r WARNING @ Tue, 30 Jun 2020 02:48:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:34: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Tue, 30 Jun 2020 02:48:34: #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 02:48:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:35: 20000000 INFO @ Tue, 30 Jun 2020 02:48:41: 21000000 INFO @ Tue, 30 Jun 2020 02:48:46: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:48:51: 23000000 INFO @ Tue, 30 Jun 2020 02:48:56: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:56: 24000000 INFO @ Tue, 30 Jun 2020 02:49:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:49:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:49:00: #1 total tags in treatment: 24539918 INFO @ Tue, 30 Jun 2020 02:49:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:00: #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 02:49:01: #1 tags after filtering in treatment: 24539859 INFO @ Tue, 30 Jun 2020 02:49:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:01: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:02: #2 number of paired peaks: 890 WARNING @ Tue, 30 Jun 2020 02:49:02: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:03: #2 predicted fragment length is 1 bps INFO @ Tue, 30 Jun 2020 02:49:03: #2 alternative fragment length(s) may be 1,48 bps INFO @ Tue, 30 Jun 2020 02:49:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.20_model.r WARNING @ Tue, 30 Jun 2020 02:49:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:03: #2 You may need to consider one of the other alternative d(s): 1,48 WARNING @ Tue, 30 Jun 2020 02:49:03: #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 02:49:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.05_summits.bed INFO @ Tue, 30 Jun 2020 02:49:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.10_summits.bed INFO @ Tue, 30 Jun 2020 02:49:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4664654/SRX4664654.20_summits.bed INFO @ Tue, 30 Jun 2020 02:49:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。