Job ID = 6458507 SRX = SRX5247957 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:36:29 prefetch.2.10.7: 1) Downloading 'SRR8440604'... 2020-06-21T12:36:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:40:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:40:30 prefetch.2.10.7: 1) 'SRR8440604' was downloaded successfully Read 25044003 spots for SRR8440604/SRR8440604.sra Written 25044003 spots for SRR8440604/SRR8440604.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: 00:06:43 25044003 reads; of these: 25044003 (100.00%) were unpaired; of these: 1354616 (5.41%) aligned 0 times 15749546 (62.89%) aligned exactly 1 time 7939841 (31.70%) aligned >1 times 94.59% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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 12 files... [bam_rmdupse_core] 2404054 / 23689387 = 0.1015 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 21:53:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.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 21:53:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:46: 1000000 INFO @ Sun, 21 Jun 2020 21:53:52: 2000000 INFO @ Sun, 21 Jun 2020 21:53:58: 3000000 INFO @ Sun, 21 Jun 2020 21:54:03: 4000000 INFO @ Sun, 21 Jun 2020 21:54:09: 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 @ Sun, 21 Jun 2020 21:54:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.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 21:54:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:14: 6000000 INFO @ Sun, 21 Jun 2020 21:54:17: 1000000 INFO @ Sun, 21 Jun 2020 21:54:20: 7000000 INFO @ Sun, 21 Jun 2020 21:54:23: 2000000 INFO @ Sun, 21 Jun 2020 21:54:26: 8000000 INFO @ Sun, 21 Jun 2020 21:54:28: 3000000 INFO @ Sun, 21 Jun 2020 21:54:32: 9000000 INFO @ Sun, 21 Jun 2020 21:54:34: 4000000 INFO @ Sun, 21 Jun 2020 21:54:38: 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 21:54:40: 5000000 INFO @ Sun, 21 Jun 2020 21:54:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.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 21:54:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:44: 11000000 INFO @ Sun, 21 Jun 2020 21:54:46: 1000000 INFO @ Sun, 21 Jun 2020 21:54:46: 6000000 INFO @ Sun, 21 Jun 2020 21:54:50: 12000000 INFO @ Sun, 21 Jun 2020 21:54:51: 2000000 INFO @ Sun, 21 Jun 2020 21:54:52: 7000000 INFO @ Sun, 21 Jun 2020 21:54:56: 13000000 INFO @ Sun, 21 Jun 2020 21:54:56: 3000000 INFO @ Sun, 21 Jun 2020 21:54:58: 8000000 INFO @ Sun, 21 Jun 2020 21:55:02: 4000000 INFO @ Sun, 21 Jun 2020 21:55:02: 14000000 INFO @ Sun, 21 Jun 2020 21:55:04: 9000000 INFO @ Sun, 21 Jun 2020 21:55:07: 5000000 INFO @ Sun, 21 Jun 2020 21:55:07: 15000000 INFO @ Sun, 21 Jun 2020 21:55:10: 10000000 INFO @ Sun, 21 Jun 2020 21:55:12: 6000000 INFO @ Sun, 21 Jun 2020 21:55:13: 16000000 INFO @ Sun, 21 Jun 2020 21:55:16: 11000000 INFO @ Sun, 21 Jun 2020 21:55:17: 7000000 INFO @ Sun, 21 Jun 2020 21:55:20: 17000000 INFO @ Sun, 21 Jun 2020 21:55:22: 12000000 INFO @ Sun, 21 Jun 2020 21:55:23: 8000000 INFO @ Sun, 21 Jun 2020 21:55:26: 18000000 INFO @ Sun, 21 Jun 2020 21:55:28: 13000000 INFO @ Sun, 21 Jun 2020 21:55:28: 9000000 INFO @ Sun, 21 Jun 2020 21:55:32: 19000000 INFO @ Sun, 21 Jun 2020 21:55:34: 10000000 INFO @ Sun, 21 Jun 2020 21:55:34: 14000000 INFO @ Sun, 21 Jun 2020 21:55:38: 20000000 INFO @ Sun, 21 Jun 2020 21:55:39: 11000000 INFO @ Sun, 21 Jun 2020 21:55:40: 15000000 INFO @ Sun, 21 Jun 2020 21:55:44: 21000000 INFO @ Sun, 21 Jun 2020 21:55:44: 12000000 INFO @ Sun, 21 Jun 2020 21:55:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:46: #1 total tags in treatment: 21285333 INFO @ Sun, 21 Jun 2020 21:55:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:46: #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 21:55:46: 16000000 INFO @ Sun, 21 Jun 2020 21:55:46: #1 tags after filtering in treatment: 21285289 INFO @ Sun, 21 Jun 2020 21:55:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:47: #2 number of paired peaks: 425 WARNING @ Sun, 21 Jun 2020 21:55:47: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:48: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:48: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:48: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:48: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:55:48: #2 alternative fragment length(s) may be 2,62,593 bps INFO @ Sun, 21 Jun 2020 21:55:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.05_model.r WARNING @ Sun, 21 Jun 2020 21:55:48: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:48: #2 You may need to consider one of the other alternative d(s): 2,62,593 WARNING @ Sun, 21 Jun 2020 21:55:48: #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 21:55:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:49: 13000000 INFO @ Sun, 21 Jun 2020 21:55:52: 17000000 INFO @ Sun, 21 Jun 2020 21:55:55: 14000000 INFO @ Sun, 21 Jun 2020 21:55:58: 18000000 INFO @ Sun, 21 Jun 2020 21:56:01: 15000000 INFO @ Sun, 21 Jun 2020 21:56:04: 19000000 INFO @ Sun, 21 Jun 2020 21:56:06: 16000000 INFO @ Sun, 21 Jun 2020 21:56:11: 20000000 INFO @ Sun, 21 Jun 2020 21:56:12: 17000000 INFO @ Sun, 21 Jun 2020 21:56:17: 18000000 INFO @ Sun, 21 Jun 2020 21:56:17: 21000000 INFO @ Sun, 21 Jun 2020 21:56:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:19: #1 total tags in treatment: 21285333 INFO @ Sun, 21 Jun 2020 21:56:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:19: #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 21:56:19: #1 tags after filtering in treatment: 21285289 INFO @ Sun, 21 Jun 2020 21:56:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:21: #2 number of paired peaks: 425 WARNING @ Sun, 21 Jun 2020 21:56:21: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:21: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:21: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:21: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:21: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:21: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:56:21: #2 alternative fragment length(s) may be 2,62,593 bps INFO @ Sun, 21 Jun 2020 21:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.10_model.r WARNING @ Sun, 21 Jun 2020 21:56:21: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:21: #2 You may need to consider one of the other alternative d(s): 2,62,593 WARNING @ Sun, 21 Jun 2020 21:56:21: #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 21:56:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:22: 19000000 INFO @ Sun, 21 Jun 2020 21:56:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:56:27: 20000000 INFO @ Sun, 21 Jun 2020 21:56:33: 21000000 INFO @ Sun, 21 Jun 2020 21:56:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:34: #1 total tags in treatment: 21285333 INFO @ Sun, 21 Jun 2020 21:56:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:34: #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 21:56:35: #1 tags after filtering in treatment: 21285289 INFO @ Sun, 21 Jun 2020 21:56:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:35: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:36: #2 number of paired peaks: 425 WARNING @ Sun, 21 Jun 2020 21:56:36: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:36: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:36: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:36: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:56:36: #2 alternative fragment length(s) may be 2,62,593 bps INFO @ Sun, 21 Jun 2020 21:56:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.20_model.r WARNING @ Sun, 21 Jun 2020 21:56:36: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:36: #2 You may need to consider one of the other alternative d(s): 2,62,593 WARNING @ Sun, 21 Jun 2020 21:56:36: #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 21:56:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.05_summits.bed INFO @ Sun, 21 Jun 2020 21:56:45: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (3233 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:57:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:57:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.10_summits.bed INFO @ Sun, 21 Jun 2020 21:57:20: Done! pass1 - making usageList (297 chroms): 1 millis pass2 - checking and writing primary data (1217 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5247957/SRX5247957.20_summits.bed INFO @ Sun, 21 Jun 2020 21:57:35: Done! pass1 - making usageList (159 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 6 millis CompletedMACS2peakCalling