Job ID = 6529869 SRX = SRX5343128 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: 00:14:32 35466474 reads; of these: 35466474 (100.00%) were unpaired; of these: 1806285 (5.09%) aligned 0 times 22904482 (64.58%) aligned exactly 1 time 10755707 (30.33%) aligned >1 times 94.91% overall alignment rate Time searching: 00:14:33 Overall time: 00:14:33 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] 5836074 / 33660189 = 0.1734 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 03:22:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.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 03:22:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:22:57: 1000000 INFO @ Tue, 30 Jun 2020 03:23:03: 2000000 INFO @ Tue, 30 Jun 2020 03:23:09: 3000000 INFO @ Tue, 30 Jun 2020 03:23:16: 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 03:23:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.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 03:23:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:23:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:22: 5000000 INFO @ Tue, 30 Jun 2020 03:23:28: 1000000 INFO @ Tue, 30 Jun 2020 03:23:29: 6000000 INFO @ Tue, 30 Jun 2020 03:23:36: 7000000 INFO @ Tue, 30 Jun 2020 03:23:36: 2000000 INFO @ Tue, 30 Jun 2020 03:23:42: 8000000 INFO @ Tue, 30 Jun 2020 03:23:44: 3000000 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 03:23:50: 9000000 INFO @ Tue, 30 Jun 2020 03:23:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.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 03:23:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:23:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:52: 4000000 INFO @ Tue, 30 Jun 2020 03:23:58: 10000000 INFO @ Tue, 30 Jun 2020 03:23:59: 1000000 INFO @ Tue, 30 Jun 2020 03:24:00: 5000000 INFO @ Tue, 30 Jun 2020 03:24:06: 11000000 INFO @ Tue, 30 Jun 2020 03:24:07: 2000000 INFO @ Tue, 30 Jun 2020 03:24:09: 6000000 INFO @ Tue, 30 Jun 2020 03:24:14: 12000000 INFO @ Tue, 30 Jun 2020 03:24:15: 3000000 INFO @ Tue, 30 Jun 2020 03:24:18: 7000000 INFO @ Tue, 30 Jun 2020 03:24:22: 13000000 INFO @ Tue, 30 Jun 2020 03:24:23: 4000000 INFO @ Tue, 30 Jun 2020 03:24:26: 8000000 INFO @ Tue, 30 Jun 2020 03:24:30: 14000000 INFO @ Tue, 30 Jun 2020 03:24:32: 5000000 INFO @ Tue, 30 Jun 2020 03:24:35: 9000000 INFO @ Tue, 30 Jun 2020 03:24:38: 15000000 INFO @ Tue, 30 Jun 2020 03:24:40: 6000000 INFO @ Tue, 30 Jun 2020 03:24:44: 10000000 INFO @ Tue, 30 Jun 2020 03:24:46: 16000000 INFO @ Tue, 30 Jun 2020 03:24:48: 7000000 INFO @ Tue, 30 Jun 2020 03:24:53: 11000000 INFO @ Tue, 30 Jun 2020 03:24:54: 17000000 INFO @ Tue, 30 Jun 2020 03:24:57: 8000000 INFO @ Tue, 30 Jun 2020 03:25:02: 18000000 INFO @ Tue, 30 Jun 2020 03:25:02: 12000000 INFO @ Tue, 30 Jun 2020 03:25:05: 9000000 INFO @ Tue, 30 Jun 2020 03:25:10: 19000000 INFO @ Tue, 30 Jun 2020 03:25:11: 13000000 INFO @ Tue, 30 Jun 2020 03:25:14: 10000000 INFO @ Tue, 30 Jun 2020 03:25:18: 20000000 INFO @ Tue, 30 Jun 2020 03:25:19: 14000000 INFO @ Tue, 30 Jun 2020 03:25:22: 11000000 INFO @ Tue, 30 Jun 2020 03:25:26: 21000000 INFO @ Tue, 30 Jun 2020 03:25:28: 15000000 INFO @ Tue, 30 Jun 2020 03:25:30: 12000000 INFO @ Tue, 30 Jun 2020 03:25:33: 22000000 INFO @ Tue, 30 Jun 2020 03:25:37: 16000000 INFO @ Tue, 30 Jun 2020 03:25:39: 13000000 INFO @ Tue, 30 Jun 2020 03:25:41: 23000000 INFO @ Tue, 30 Jun 2020 03:25:45: 17000000 INFO @ Tue, 30 Jun 2020 03:25:47: 14000000 INFO @ Tue, 30 Jun 2020 03:25:50: 24000000 INFO @ Tue, 30 Jun 2020 03:25:54: 18000000 INFO @ Tue, 30 Jun 2020 03:25:55: 15000000 INFO @ Tue, 30 Jun 2020 03:25:58: 25000000 INFO @ Tue, 30 Jun 2020 03:26:02: 19000000 INFO @ Tue, 30 Jun 2020 03:26:04: 16000000 INFO @ Tue, 30 Jun 2020 03:26:06: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:26:11: 20000000 INFO @ Tue, 30 Jun 2020 03:26:12: 17000000 INFO @ Tue, 30 Jun 2020 03:26:14: 27000000 INFO @ Tue, 30 Jun 2020 03:26:19: 21000000 INFO @ Tue, 30 Jun 2020 03:26:20: 18000000 INFO @ Tue, 30 Jun 2020 03:26:21: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:26:21: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:26:21: #1 total tags in treatment: 27824115 INFO @ Tue, 30 Jun 2020 03:26:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:26:21: #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 03:26:21: #1 tags after filtering in treatment: 27824114 INFO @ Tue, 30 Jun 2020 03:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:26:21: #1 finished! INFO @ Tue, 30 Jun 2020 03:26:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:26:23: #2 number of paired peaks: 205 WARNING @ Tue, 30 Jun 2020 03:26:23: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 30 Jun 2020 03:26:23: start model_add_line... INFO @ Tue, 30 Jun 2020 03:26:24: start X-correlation... INFO @ Tue, 30 Jun 2020 03:26:24: end of X-cor INFO @ Tue, 30 Jun 2020 03:26:24: #2 finished! INFO @ Tue, 30 Jun 2020 03:26:24: #2 predicted fragment length is 60 bps INFO @ Tue, 30 Jun 2020 03:26:24: #2 alternative fragment length(s) may be 2,60,578 bps INFO @ Tue, 30 Jun 2020 03:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.05_model.r WARNING @ Tue, 30 Jun 2020 03:26:24: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:26:24: #2 You may need to consider one of the other alternative d(s): 2,60,578 WARNING @ Tue, 30 Jun 2020 03:26:24: #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 03:26:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:26:28: 22000000 INFO @ Tue, 30 Jun 2020 03:26:28: 19000000 INFO @ Tue, 30 Jun 2020 03:26:37: 20000000 INFO @ Tue, 30 Jun 2020 03:26:37: 23000000 INFO @ Tue, 30 Jun 2020 03:26:45: 21000000 INFO @ Tue, 30 Jun 2020 03:26:46: 24000000 INFO @ Tue, 30 Jun 2020 03:26:53: 22000000 INFO @ Tue, 30 Jun 2020 03:26:55: 25000000 INFO @ Tue, 30 Jun 2020 03:27:01: 23000000 INFO @ Tue, 30 Jun 2020 03:27:03: 26000000 INFO @ Tue, 30 Jun 2020 03:27:10: 24000000 INFO @ Tue, 30 Jun 2020 03:27:12: 27000000 INFO @ Tue, 30 Jun 2020 03:27:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:27:18: 25000000 INFO @ Tue, 30 Jun 2020 03:27:18: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:27:18: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:27:18: #1 total tags in treatment: 27824115 INFO @ Tue, 30 Jun 2020 03:27:18: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:18: #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 03:27:19: #1 tags after filtering in treatment: 27824114 INFO @ Tue, 30 Jun 2020 03:27:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:19: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:19: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:27:21: #2 number of paired peaks: 205 WARNING @ Tue, 30 Jun 2020 03:27:21: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 30 Jun 2020 03:27:21: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:21: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:21: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:21: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:21: #2 predicted fragment length is 60 bps INFO @ Tue, 30 Jun 2020 03:27:21: #2 alternative fragment length(s) may be 2,60,578 bps INFO @ Tue, 30 Jun 2020 03:27:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.10_model.r WARNING @ Tue, 30 Jun 2020 03:27:21: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:21: #2 You may need to consider one of the other alternative d(s): 2,60,578 WARNING @ Tue, 30 Jun 2020 03:27:21: #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 03:27:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:27:25: 26000000 INFO @ Tue, 30 Jun 2020 03:27:33: 27000000 INFO @ Tue, 30 Jun 2020 03:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.05_summits.bed INFO @ Tue, 30 Jun 2020 03:27:37: Done! pass1 - making usageList (779 chroms): 2 millis pass2 - checking and writing primary data (2572 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:27:39: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:27:39: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:27:39: #1 total tags in treatment: 27824115 INFO @ Tue, 30 Jun 2020 03:27:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:39: #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 03:27:40: #1 tags after filtering in treatment: 27824114 INFO @ Tue, 30 Jun 2020 03:27:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:40: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:27:41: #2 number of paired peaks: 205 WARNING @ Tue, 30 Jun 2020 03:27:41: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Tue, 30 Jun 2020 03:27:41: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:42: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:42: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:42: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:42: #2 predicted fragment length is 60 bps INFO @ Tue, 30 Jun 2020 03:27:42: #2 alternative fragment length(s) may be 2,60,578 bps INFO @ Tue, 30 Jun 2020 03:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.20_model.r WARNING @ Tue, 30 Jun 2020 03:27:42: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:42: #2 You may need to consider one of the other alternative d(s): 2,60,578 WARNING @ Tue, 30 Jun 2020 03:27:42: #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 03:27:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:28:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:28:28: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:28:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.10_summits.bed INFO @ Tue, 30 Jun 2020 03:28:31: Done! pass1 - making usageList (617 chroms): 1 millis pass2 - checking and writing primary data (1893 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343128/SRX5343128.20_summits.bed INFO @ Tue, 30 Jun 2020 03:28:50: Done! pass1 - making usageList (434 chroms): 1 millis pass2 - checking and writing primary data (1058 records, 4 fields): 14 millis CompletedMACS2peakCalling