Job ID = 6456067 SRX = SRX3167245 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:30:36 prefetch.2.10.7: 1) Downloading 'SRR6014248'... 2020-06-21T10:30:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:48:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:48:53 prefetch.2.10.7: 1) 'SRR6014248' was downloaded successfully Read 75175147 spots for SRR6014248/SRR6014248.sra Written 75175147 spots for SRR6014248/SRR6014248.sra 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: 00:28:48 75175147 reads; of these: 75175147 (100.00%) were unpaired; of these: 4229452 (5.63%) aligned 0 times 41715423 (55.49%) aligned exactly 1 time 29230272 (38.88%) aligned >1 times 94.37% overall alignment rate Time searching: 00:28:48 Overall time: 00:28:48 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 32 files... [bam_rmdupse_core] 45289347 / 70945695 = 0.6384 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 @ Sun, 21 Jun 2020 20:34:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.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 @ Sun, 21 Jun 2020 20:34:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:52: 1000000 INFO @ Sun, 21 Jun 2020 20:34:58: 2000000 INFO @ Sun, 21 Jun 2020 20:35:04: 3000000 INFO @ Sun, 21 Jun 2020 20:35:10: 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 @ Sun, 21 Jun 2020 20:35:16: 5000000 INFO @ Sun, 21 Jun 2020 20:35:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.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 @ Sun, 21 Jun 2020 20:35:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:21: 6000000 INFO @ Sun, 21 Jun 2020 20:35:23: 1000000 INFO @ Sun, 21 Jun 2020 20:35:27: 7000000 INFO @ Sun, 21 Jun 2020 20:35:29: 2000000 INFO @ Sun, 21 Jun 2020 20:35:33: 8000000 INFO @ Sun, 21 Jun 2020 20:35:35: 3000000 INFO @ Sun, 21 Jun 2020 20:35:39: 9000000 INFO @ Sun, 21 Jun 2020 20:35:40: 4000000 INFO @ Sun, 21 Jun 2020 20:35:44: 10000000 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 @ Sun, 21 Jun 2020 20:35:46: 5000000 INFO @ Sun, 21 Jun 2020 20:35:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.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 @ Sun, 21 Jun 2020 20:35:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:50: 11000000 INFO @ Sun, 21 Jun 2020 20:35:52: 6000000 INFO @ Sun, 21 Jun 2020 20:35:52: 1000000 INFO @ Sun, 21 Jun 2020 20:35:56: 12000000 INFO @ Sun, 21 Jun 2020 20:35:58: 2000000 INFO @ Sun, 21 Jun 2020 20:35:58: 7000000 INFO @ Sun, 21 Jun 2020 20:36:01: 13000000 INFO @ Sun, 21 Jun 2020 20:36:04: 3000000 INFO @ Sun, 21 Jun 2020 20:36:04: 8000000 INFO @ Sun, 21 Jun 2020 20:36:07: 14000000 INFO @ Sun, 21 Jun 2020 20:36:09: 4000000 INFO @ Sun, 21 Jun 2020 20:36:10: 9000000 INFO @ Sun, 21 Jun 2020 20:36:13: 15000000 INFO @ Sun, 21 Jun 2020 20:36:14: 5000000 INFO @ Sun, 21 Jun 2020 20:36:15: 10000000 INFO @ Sun, 21 Jun 2020 20:36:18: 16000000 INFO @ Sun, 21 Jun 2020 20:36:19: 6000000 INFO @ Sun, 21 Jun 2020 20:36:21: 11000000 INFO @ Sun, 21 Jun 2020 20:36:24: 17000000 INFO @ Sun, 21 Jun 2020 20:36:24: 7000000 INFO @ Sun, 21 Jun 2020 20:36:27: 12000000 INFO @ Sun, 21 Jun 2020 20:36:30: 8000000 INFO @ Sun, 21 Jun 2020 20:36:30: 18000000 INFO @ Sun, 21 Jun 2020 20:36:32: 13000000 INFO @ Sun, 21 Jun 2020 20:36:35: 9000000 INFO @ Sun, 21 Jun 2020 20:36:35: 19000000 INFO @ Sun, 21 Jun 2020 20:36:38: 14000000 INFO @ Sun, 21 Jun 2020 20:36:40: 10000000 INFO @ Sun, 21 Jun 2020 20:36:41: 20000000 INFO @ Sun, 21 Jun 2020 20:36:43: 15000000 INFO @ Sun, 21 Jun 2020 20:36:45: 11000000 INFO @ Sun, 21 Jun 2020 20:36:47: 21000000 INFO @ Sun, 21 Jun 2020 20:36:49: 16000000 INFO @ Sun, 21 Jun 2020 20:36:50: 12000000 INFO @ Sun, 21 Jun 2020 20:36:53: 22000000 INFO @ Sun, 21 Jun 2020 20:36:55: 13000000 INFO @ Sun, 21 Jun 2020 20:36:55: 17000000 INFO @ Sun, 21 Jun 2020 20:36:58: 23000000 INFO @ Sun, 21 Jun 2020 20:37:00: 14000000 INFO @ Sun, 21 Jun 2020 20:37:01: 18000000 INFO @ Sun, 21 Jun 2020 20:37:04: 24000000 INFO @ Sun, 21 Jun 2020 20:37:05: 15000000 INFO @ Sun, 21 Jun 2020 20:37:06: 19000000 INFO @ Sun, 21 Jun 2020 20:37:10: 25000000 INFO @ Sun, 21 Jun 2020 20:37:10: 16000000 INFO @ Sun, 21 Jun 2020 20:37:12: 20000000 INFO @ Sun, 21 Jun 2020 20:37:14: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:37:14: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:37:14: #1 total tags in treatment: 25656348 INFO @ Sun, 21 Jun 2020 20:37:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:37:14: #1 tags after filtering in treatment: 25656300 INFO @ Sun, 21 Jun 2020 20:37:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:15: 17000000 INFO @ Sun, 21 Jun 2020 20:37:16: #2 number of paired peaks: 638 WARNING @ Sun, 21 Jun 2020 20:37:16: Fewer paired peaks (638) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 638 pairs to build model! INFO @ Sun, 21 Jun 2020 20:37:16: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:16: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 20:37:16: #2 alternative fragment length(s) may be 2,54 bps INFO @ Sun, 21 Jun 2020 20:37:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.05_model.r WARNING @ Sun, 21 Jun 2020 20:37:16: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:37:16: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Sun, 21 Jun 2020 20:37:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:37:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:18: 21000000 INFO @ Sun, 21 Jun 2020 20:37:20: 18000000 INFO @ Sun, 21 Jun 2020 20:37:24: 22000000 INFO @ Sun, 21 Jun 2020 20:37:25: 19000000 INFO @ Sun, 21 Jun 2020 20:37:29: 23000000 INFO @ Sun, 21 Jun 2020 20:37:30: 20000000 INFO @ Sun, 21 Jun 2020 20:37:35: 24000000 INFO @ Sun, 21 Jun 2020 20:37:35: 21000000 INFO @ Sun, 21 Jun 2020 20:37:40: 22000000 INFO @ Sun, 21 Jun 2020 20:37:41: 25000000 INFO @ Sun, 21 Jun 2020 20:37:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:37:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:37:45: #1 total tags in treatment: 25656348 INFO @ Sun, 21 Jun 2020 20:37:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:37:45: 23000000 INFO @ Sun, 21 Jun 2020 20:37:45: #1 tags after filtering in treatment: 25656300 INFO @ Sun, 21 Jun 2020 20:37:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:45: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:45: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:37:47: #2 number of paired peaks: 638 WARNING @ Sun, 21 Jun 2020 20:37:47: Fewer paired peaks (638) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 638 pairs to build model! INFO @ Sun, 21 Jun 2020 20:37:47: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:47: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:47: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:47: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:47: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 20:37:47: #2 alternative fragment length(s) may be 2,54 bps INFO @ Sun, 21 Jun 2020 20:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.10_model.r WARNING @ Sun, 21 Jun 2020 20:37:47: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:37:47: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Sun, 21 Jun 2020 20:37:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:37:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:50: 24000000 INFO @ Sun, 21 Jun 2020 20:37:55: 25000000 INFO @ Sun, 21 Jun 2020 20:37:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:37:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:37:59: #1 total tags in treatment: 25656348 INFO @ Sun, 21 Jun 2020 20:37:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 20:37:59: #1 tags after filtering in treatment: 25656300 INFO @ Sun, 21 Jun 2020 20:37:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:59: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:38:01: #2 number of paired peaks: 638 WARNING @ Sun, 21 Jun 2020 20:38:01: Fewer paired peaks (638) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 638 pairs to build model! INFO @ Sun, 21 Jun 2020 20:38:01: start model_add_line... INFO @ Sun, 21 Jun 2020 20:38:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:38:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:38:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:38:01: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 20:38:01: #2 alternative fragment length(s) may be 2,54 bps INFO @ Sun, 21 Jun 2020 20:38:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.20_model.r WARNING @ Sun, 21 Jun 2020 20:38:01: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:38:01: #2 You may need to consider one of the other alternative d(s): 2,54 WARNING @ Sun, 21 Jun 2020 20:38:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 20:38:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:38:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.05_summits.bed INFO @ Sun, 21 Jun 2020 20:38:23: Done! pass1 - making usageList (852 chroms): 2 millis pass2 - checking and writing primary data (9217 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:38:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:38:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.10_summits.bed INFO @ Sun, 21 Jun 2020 20:38:52: Done! pass1 - making usageList (664 chroms): 1 millis pass2 - checking and writing primary data (3733 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:39:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:39:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:39:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3167245/SRX3167245.20_summits.bed INFO @ Sun, 21 Jun 2020 20:39:11: Done! pass1 - making usageList (355 chroms): 1 millis pass2 - checking and writing primary data (1097 records, 4 fields): 11 millis CompletedMACS2peakCalling