Job ID = 6527489 SRX = SRX032114 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:50:57 prefetch.2.10.7: 1) Downloading 'SRR073933'... 2020-06-29T12:50:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:52:56 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:52:57 prefetch.2.10.7: 'SRR073933' is valid 2020-06-29T12:52:57 prefetch.2.10.7: 1) 'SRR073933' was downloaded successfully Read 21984902 spots for SRR073933/SRR073933.sra Written 21984902 spots for SRR073933/SRR073933.sra 2020-06-29T12:54:08 prefetch.2.10.7: 1) Downloading 'SRR073934'... 2020-06-29T12:54:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:55:32 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:55:33 prefetch.2.10.7: 'SRR073934' is valid 2020-06-29T12:55:33 prefetch.2.10.7: 1) 'SRR073934' was downloaded successfully Read 22378029 spots for SRR073934/SRR073934.sra Written 22378029 spots for SRR073934/SRR073934.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: 00:25:33 44362931 reads; of these: 44362931 (100.00%) were unpaired; of these: 607568 (1.37%) aligned 0 times 14981877 (33.77%) aligned exactly 1 time 28773486 (64.86%) aligned >1 times 98.63% overall alignment rate Time searching: 00:25:33 Overall time: 00:25:33 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14722295 / 43755363 = 0.3365 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 @ Mon, 29 Jun 2020 22:38:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.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 @ Mon, 29 Jun 2020 22:38:41: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:38:41: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:38:46: 1000000 INFO @ Mon, 29 Jun 2020 22:38:50: 2000000 INFO @ Mon, 29 Jun 2020 22:38:55: 3000000 INFO @ Mon, 29 Jun 2020 22:39:00: 4000000 INFO @ Mon, 29 Jun 2020 22:39:05: 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 @ Mon, 29 Jun 2020 22:39:09: 6000000 INFO @ Mon, 29 Jun 2020 22:39:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.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 @ Mon, 29 Jun 2020 22:39:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:39:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:39:14: 7000000 INFO @ Mon, 29 Jun 2020 22:39:16: 1000000 INFO @ Mon, 29 Jun 2020 22:39:19: 8000000 INFO @ Mon, 29 Jun 2020 22:39:21: 2000000 INFO @ Mon, 29 Jun 2020 22:39:24: 9000000 INFO @ Mon, 29 Jun 2020 22:39:27: 3000000 INFO @ Mon, 29 Jun 2020 22:39:29: 10000000 INFO @ Mon, 29 Jun 2020 22:39:32: 4000000 INFO @ Mon, 29 Jun 2020 22:39:34: 11000000 INFO @ Mon, 29 Jun 2020 22:39:37: 5000000 INFO @ Mon, 29 Jun 2020 22:39:39: 12000000 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 @ Mon, 29 Jun 2020 22:39:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.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 @ Mon, 29 Jun 2020 22:39:41: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:39:41: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:39:42: 6000000 INFO @ Mon, 29 Jun 2020 22:39:44: 13000000 INFO @ Mon, 29 Jun 2020 22:39:47: 1000000 INFO @ Mon, 29 Jun 2020 22:39:47: 7000000 INFO @ Mon, 29 Jun 2020 22:39:49: 14000000 INFO @ Mon, 29 Jun 2020 22:39:52: 2000000 INFO @ Mon, 29 Jun 2020 22:39:53: 8000000 INFO @ Mon, 29 Jun 2020 22:39:54: 15000000 INFO @ Mon, 29 Jun 2020 22:39:58: 3000000 INFO @ Mon, 29 Jun 2020 22:39:58: 9000000 INFO @ Mon, 29 Jun 2020 22:39:59: 16000000 INFO @ Mon, 29 Jun 2020 22:40:03: 4000000 INFO @ Mon, 29 Jun 2020 22:40:04: 10000000 INFO @ Mon, 29 Jun 2020 22:40:04: 17000000 INFO @ Mon, 29 Jun 2020 22:40:09: 18000000 INFO @ Mon, 29 Jun 2020 22:40:09: 5000000 INFO @ Mon, 29 Jun 2020 22:40:09: 11000000 INFO @ Mon, 29 Jun 2020 22:40:14: 19000000 INFO @ Mon, 29 Jun 2020 22:40:14: 6000000 INFO @ Mon, 29 Jun 2020 22:40:14: 12000000 INFO @ Mon, 29 Jun 2020 22:40:19: 20000000 INFO @ Mon, 29 Jun 2020 22:40:20: 7000000 INFO @ Mon, 29 Jun 2020 22:40:20: 13000000 INFO @ Mon, 29 Jun 2020 22:40:24: 21000000 INFO @ Mon, 29 Jun 2020 22:40:25: 14000000 INFO @ Mon, 29 Jun 2020 22:40:25: 8000000 INFO @ Mon, 29 Jun 2020 22:40:28: 22000000 INFO @ Mon, 29 Jun 2020 22:40:31: 15000000 INFO @ Mon, 29 Jun 2020 22:40:31: 9000000 INFO @ Mon, 29 Jun 2020 22:40:33: 23000000 INFO @ Mon, 29 Jun 2020 22:40:36: 16000000 INFO @ Mon, 29 Jun 2020 22:40:37: 10000000 INFO @ Mon, 29 Jun 2020 22:40:38: 24000000 INFO @ Mon, 29 Jun 2020 22:40:42: 17000000 INFO @ Mon, 29 Jun 2020 22:40:42: 11000000 INFO @ Mon, 29 Jun 2020 22:40:43: 25000000 INFO @ Mon, 29 Jun 2020 22:40:47: 18000000 INFO @ Mon, 29 Jun 2020 22:40:48: 12000000 INFO @ Mon, 29 Jun 2020 22:40:48: 26000000 INFO @ Mon, 29 Jun 2020 22:40:52: 19000000 INFO @ Mon, 29 Jun 2020 22:40:53: 27000000 INFO @ Mon, 29 Jun 2020 22:40:54: 13000000 INFO @ Mon, 29 Jun 2020 22:40:58: 20000000 INFO @ Mon, 29 Jun 2020 22:40:58: 28000000 INFO @ Mon, 29 Jun 2020 22:40:59: 14000000 INFO @ Mon, 29 Jun 2020 22:41:03: 29000000 INFO @ Mon, 29 Jun 2020 22:41:03: 21000000 INFO @ Mon, 29 Jun 2020 22:41:03: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:41:03: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:41:03: #1 total tags in treatment: 29033068 INFO @ Mon, 29 Jun 2020 22:41:03: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:41:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:41:04: #1 tags after filtering in treatment: 29033068 INFO @ Mon, 29 Jun 2020 22:41:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:41:04: #1 finished! INFO @ Mon, 29 Jun 2020 22:41:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:41:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:41:05: 15000000 INFO @ Mon, 29 Jun 2020 22:41:06: #2 number of paired peaks: 250 WARNING @ Mon, 29 Jun 2020 22:41:06: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Mon, 29 Jun 2020 22:41:06: start model_add_line... INFO @ Mon, 29 Jun 2020 22:41:06: start X-correlation... INFO @ Mon, 29 Jun 2020 22:41:06: end of X-cor INFO @ Mon, 29 Jun 2020 22:41:06: #2 finished! INFO @ Mon, 29 Jun 2020 22:41:06: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:41:06: #2 alternative fragment length(s) may be 4,33 bps INFO @ Mon, 29 Jun 2020 22:41:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.05_model.r WARNING @ Mon, 29 Jun 2020 22:41:06: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:41:06: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Mon, 29 Jun 2020 22:41:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:41:06: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:41:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:41:09: 22000000 INFO @ Mon, 29 Jun 2020 22:41:10: 16000000 INFO @ Mon, 29 Jun 2020 22:41:14: 23000000 INFO @ Mon, 29 Jun 2020 22:41:16: 17000000 INFO @ Mon, 29 Jun 2020 22:41:19: 24000000 INFO @ Mon, 29 Jun 2020 22:41:21: 18000000 INFO @ Mon, 29 Jun 2020 22:41:25: 25000000 INFO @ Mon, 29 Jun 2020 22:41:26: 19000000 INFO @ Mon, 29 Jun 2020 22:41:30: 26000000 INFO @ Mon, 29 Jun 2020 22:41:32: 20000000 INFO @ Mon, 29 Jun 2020 22:41:35: 27000000 INFO @ Mon, 29 Jun 2020 22:41:37: 21000000 INFO @ Mon, 29 Jun 2020 22:41:41: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:41:43: 22000000 INFO @ Mon, 29 Jun 2020 22:41:46: 29000000 INFO @ Mon, 29 Jun 2020 22:41:46: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:41:46: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:41:46: #1 total tags in treatment: 29033068 INFO @ Mon, 29 Jun 2020 22:41:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:41:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:41:47: #1 tags after filtering in treatment: 29033068 INFO @ Mon, 29 Jun 2020 22:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:41:47: #1 finished! INFO @ Mon, 29 Jun 2020 22:41:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:41:48: 23000000 INFO @ Mon, 29 Jun 2020 22:41:49: #2 number of paired peaks: 250 WARNING @ Mon, 29 Jun 2020 22:41:49: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Mon, 29 Jun 2020 22:41:49: start model_add_line... INFO @ Mon, 29 Jun 2020 22:41:49: start X-correlation... INFO @ Mon, 29 Jun 2020 22:41:49: end of X-cor INFO @ Mon, 29 Jun 2020 22:41:49: #2 finished! INFO @ Mon, 29 Jun 2020 22:41:49: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:41:49: #2 alternative fragment length(s) may be 4,33 bps INFO @ Mon, 29 Jun 2020 22:41:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.10_model.r WARNING @ Mon, 29 Jun 2020 22:41:49: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:41:49: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Mon, 29 Jun 2020 22:41:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:41:49: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:41:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:41:53: 24000000 INFO @ Mon, 29 Jun 2020 22:41:57: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:41:59: 25000000 INFO @ Mon, 29 Jun 2020 22:42:04: 26000000 INFO @ Mon, 29 Jun 2020 22:42:09: 27000000 INFO @ Mon, 29 Jun 2020 22:42:15: 28000000 INFO @ Mon, 29 Jun 2020 22:42:20: 29000000 INFO @ Mon, 29 Jun 2020 22:42:21: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:42:21: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:42:21: #1 total tags in treatment: 29033068 INFO @ Mon, 29 Jun 2020 22:42:21: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:42:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:42:21: #1 tags after filtering in treatment: 29033068 INFO @ Mon, 29 Jun 2020 22:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:42:21: #1 finished! INFO @ Mon, 29 Jun 2020 22:42:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.05_summits.bed INFO @ Mon, 29 Jun 2020 22:42:23: Done! INFO @ Mon, 29 Jun 2020 22:42:23: #2 number of paired peaks: 250 WARNING @ Mon, 29 Jun 2020 22:42:23: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Mon, 29 Jun 2020 22:42:23: start model_add_line... INFO @ Mon, 29 Jun 2020 22:42:23: start X-correlation... INFO @ Mon, 29 Jun 2020 22:42:23: end of X-cor INFO @ Mon, 29 Jun 2020 22:42:23: #2 finished! INFO @ Mon, 29 Jun 2020 22:42:23: #2 predicted fragment length is 33 bps INFO @ Mon, 29 Jun 2020 22:42:23: #2 alternative fragment length(s) may be 4,33 bps INFO @ Mon, 29 Jun 2020 22:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.20_model.r WARNING @ Mon, 29 Jun 2020 22:42:23: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:42:23: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Mon, 29 Jun 2020 22:42:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:42:23: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:42:23: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5418 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:42:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:43:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:43:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:43:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.10_summits.bed INFO @ Mon, 29 Jun 2020 22:43:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2248 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:43:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032114/SRX032114.20_summits.bed INFO @ Mon, 29 Jun 2020 22:43:41: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1035 records, 4 fields): 3 millis CompletedMACS2peakCalling