Job ID = 6527482 SRX = SRX026864 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:52:42 prefetch.2.10.7: 1) Downloading 'SRR065764'... 2020-06-29T12:52:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:54:40 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:54:41 prefetch.2.10.7: 'SRR065764' is valid 2020-06-29T12:54:41 prefetch.2.10.7: 1) 'SRR065764' was downloaded successfully Read 22087059 spots for SRR065764/SRR065764.sra Written 22087059 spots for SRR065764/SRR065764.sra 2020-06-29T12:55:50 prefetch.2.10.7: 1) Downloading 'SRR065765'... 2020-06-29T12:55:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:57:27 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:57:28 prefetch.2.10.7: 'SRR065765' is valid 2020-06-29T12:57:28 prefetch.2.10.7: 1) 'SRR065765' was downloaded successfully Read 24424901 spots for SRR065765/SRR065765.sra Written 24424901 spots for SRR065765/SRR065765.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: 00:15:40 46511960 reads; of these: 46511960 (100.00%) were unpaired; of these: 1770005 (3.81%) aligned 0 times 31290850 (67.27%) aligned exactly 1 time 13451105 (28.92%) aligned >1 times 96.19% overall alignment rate Time searching: 00:15:40 Overall time: 00:15:40 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] 18468382 / 44741955 = 0.4128 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 22:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.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 22:32:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:32:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:32:11: 1000000 INFO @ Mon, 29 Jun 2020 22:32:17: 2000000 INFO @ Mon, 29 Jun 2020 22:32:24: 3000000 INFO @ Mon, 29 Jun 2020 22:32:30: 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 @ Mon, 29 Jun 2020 22:32:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.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 22:32:33: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:32:33: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:32:37: 5000000 INFO @ Mon, 29 Jun 2020 22:32:39: 1000000 INFO @ Mon, 29 Jun 2020 22:32:44: 6000000 INFO @ Mon, 29 Jun 2020 22:32:46: 2000000 INFO @ Mon, 29 Jun 2020 22:32:51: 7000000 INFO @ Mon, 29 Jun 2020 22:32:53: 3000000 INFO @ Mon, 29 Jun 2020 22:32:58: 8000000 INFO @ Mon, 29 Jun 2020 22:33:00: 4000000 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 22:33:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.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 22:33:03: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:33:03: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:33:05: 9000000 INFO @ Mon, 29 Jun 2020 22:33:06: 5000000 INFO @ Mon, 29 Jun 2020 22:33:09: 1000000 INFO @ Mon, 29 Jun 2020 22:33:11: 10000000 INFO @ Mon, 29 Jun 2020 22:33:13: 6000000 INFO @ Mon, 29 Jun 2020 22:33:16: 2000000 INFO @ Mon, 29 Jun 2020 22:33:18: 11000000 INFO @ Mon, 29 Jun 2020 22:33:20: 7000000 INFO @ Mon, 29 Jun 2020 22:33:22: 3000000 INFO @ Mon, 29 Jun 2020 22:33:25: 12000000 INFO @ Mon, 29 Jun 2020 22:33:27: 8000000 INFO @ Mon, 29 Jun 2020 22:33:29: 4000000 INFO @ Mon, 29 Jun 2020 22:33:32: 13000000 INFO @ Mon, 29 Jun 2020 22:33:34: 9000000 INFO @ Mon, 29 Jun 2020 22:33:35: 5000000 INFO @ Mon, 29 Jun 2020 22:33:39: 14000000 INFO @ Mon, 29 Jun 2020 22:33:40: 10000000 INFO @ Mon, 29 Jun 2020 22:33:42: 6000000 INFO @ Mon, 29 Jun 2020 22:33:46: 15000000 INFO @ Mon, 29 Jun 2020 22:33:47: 11000000 INFO @ Mon, 29 Jun 2020 22:33:48: 7000000 INFO @ Mon, 29 Jun 2020 22:33:53: 16000000 INFO @ Mon, 29 Jun 2020 22:33:54: 12000000 INFO @ Mon, 29 Jun 2020 22:33:54: 8000000 INFO @ Mon, 29 Jun 2020 22:33:59: 17000000 INFO @ Mon, 29 Jun 2020 22:34:00: 13000000 INFO @ Mon, 29 Jun 2020 22:34:01: 9000000 INFO @ Mon, 29 Jun 2020 22:34:06: 18000000 INFO @ Mon, 29 Jun 2020 22:34:07: 10000000 INFO @ Mon, 29 Jun 2020 22:34:07: 14000000 INFO @ Mon, 29 Jun 2020 22:34:13: 11000000 INFO @ Mon, 29 Jun 2020 22:34:13: 19000000 INFO @ Mon, 29 Jun 2020 22:34:14: 15000000 INFO @ Mon, 29 Jun 2020 22:34:19: 12000000 INFO @ Mon, 29 Jun 2020 22:34:20: 20000000 INFO @ Mon, 29 Jun 2020 22:34:21: 16000000 INFO @ Mon, 29 Jun 2020 22:34:26: 13000000 INFO @ Mon, 29 Jun 2020 22:34:27: 21000000 INFO @ Mon, 29 Jun 2020 22:34:27: 17000000 INFO @ Mon, 29 Jun 2020 22:34:32: 14000000 INFO @ Mon, 29 Jun 2020 22:34:34: 18000000 INFO @ Mon, 29 Jun 2020 22:34:34: 22000000 INFO @ Mon, 29 Jun 2020 22:34:38: 15000000 INFO @ Mon, 29 Jun 2020 22:34:41: 19000000 INFO @ Mon, 29 Jun 2020 22:34:41: 23000000 INFO @ Mon, 29 Jun 2020 22:34:45: 16000000 INFO @ Mon, 29 Jun 2020 22:34:48: 20000000 INFO @ Mon, 29 Jun 2020 22:34:48: 24000000 INFO @ Mon, 29 Jun 2020 22:34:51: 17000000 INFO @ Mon, 29 Jun 2020 22:34:54: 21000000 INFO @ Mon, 29 Jun 2020 22:34:55: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:34:57: 18000000 INFO @ Mon, 29 Jun 2020 22:35:01: 22000000 INFO @ Mon, 29 Jun 2020 22:35:02: 26000000 INFO @ Mon, 29 Jun 2020 22:35:03: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:35:03: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:35:03: #1 total tags in treatment: 26273573 INFO @ Mon, 29 Jun 2020 22:35:03: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:35:03: #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 22:35:04: 19000000 INFO @ Mon, 29 Jun 2020 22:35:04: #1 tags after filtering in treatment: 26273573 INFO @ Mon, 29 Jun 2020 22:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:35:04: #1 finished! INFO @ Mon, 29 Jun 2020 22:35:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:35:06: #2 number of paired peaks: 114 WARNING @ Mon, 29 Jun 2020 22:35:06: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 29 Jun 2020 22:35:06: start model_add_line... INFO @ Mon, 29 Jun 2020 22:35:06: start X-correlation... INFO @ Mon, 29 Jun 2020 22:35:06: end of X-cor INFO @ Mon, 29 Jun 2020 22:35:06: #2 finished! INFO @ Mon, 29 Jun 2020 22:35:06: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 22:35:06: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 22:35:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.05_model.r WARNING @ Mon, 29 Jun 2020 22:35:06: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:35:06: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 22:35:06: #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 22:35:06: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:35:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:35:08: 23000000 INFO @ Mon, 29 Jun 2020 22:35:10: 20000000 INFO @ Mon, 29 Jun 2020 22:35:15: 24000000 INFO @ Mon, 29 Jun 2020 22:35:16: 21000000 INFO @ Mon, 29 Jun 2020 22:35:22: 25000000 INFO @ Mon, 29 Jun 2020 22:35:22: 22000000 INFO @ Mon, 29 Jun 2020 22:35:28: 26000000 INFO @ Mon, 29 Jun 2020 22:35:28: 23000000 INFO @ Mon, 29 Jun 2020 22:35:30: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:35:30: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:35:30: #1 total tags in treatment: 26273573 INFO @ Mon, 29 Jun 2020 22:35:30: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:35:30: #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 22:35:31: #1 tags after filtering in treatment: 26273573 INFO @ Mon, 29 Jun 2020 22:35:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:35:31: #1 finished! INFO @ Mon, 29 Jun 2020 22:35:31: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:35:32: #2 number of paired peaks: 114 WARNING @ Mon, 29 Jun 2020 22:35:32: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 29 Jun 2020 22:35:32: start model_add_line... INFO @ Mon, 29 Jun 2020 22:35:32: start X-correlation... INFO @ Mon, 29 Jun 2020 22:35:32: end of X-cor INFO @ Mon, 29 Jun 2020 22:35:32: #2 finished! INFO @ Mon, 29 Jun 2020 22:35:32: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 22:35:32: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 22:35:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.10_model.r WARNING @ Mon, 29 Jun 2020 22:35:32: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:35:32: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 22:35:32: #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 22:35:32: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:35:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:35:34: 24000000 INFO @ Mon, 29 Jun 2020 22:35:40: 25000000 INFO @ Mon, 29 Jun 2020 22:35:45: 26000000 INFO @ Mon, 29 Jun 2020 22:35:47: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:35:47: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:35:47: #1 total tags in treatment: 26273573 INFO @ Mon, 29 Jun 2020 22:35:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:35:47: #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 22:35:47: #1 tags after filtering in treatment: 26273573 INFO @ Mon, 29 Jun 2020 22:35:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:35:47: #1 finished! INFO @ Mon, 29 Jun 2020 22:35:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:35:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:35:49: #2 number of paired peaks: 114 WARNING @ Mon, 29 Jun 2020 22:35:49: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 29 Jun 2020 22:35:49: start model_add_line... INFO @ Mon, 29 Jun 2020 22:35:49: start X-correlation... INFO @ Mon, 29 Jun 2020 22:35:49: end of X-cor INFO @ Mon, 29 Jun 2020 22:35:49: #2 finished! INFO @ Mon, 29 Jun 2020 22:35:49: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 22:35:49: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 22:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.20_model.r WARNING @ Mon, 29 Jun 2020 22:35:49: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:35:49: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 22:35:49: #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 22:35:49: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:35:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.05_summits.bed INFO @ Mon, 29 Jun 2020 22:36:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2809 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:36:20: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:36:38: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:36:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:36:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:36:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.10_summits.bed INFO @ Mon, 29 Jun 2020 22:36:43: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1853 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX026864/SRX026864.20_summits.bed INFO @ Mon, 29 Jun 2020 22:37:02: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1102 records, 4 fields): 2 millis CompletedMACS2peakCalling