Job ID = 6527661 SRX = SRX193328 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:13:23 prefetch.2.10.7: 1) Downloading 'SRR585061'... 2020-06-29T13:13:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:18:48 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:18:48 prefetch.2.10.7: 1) 'SRR585061' was downloaded successfully Read 35151074 spots for SRR585061/SRR585061.sra Written 35151074 spots for SRR585061/SRR585061.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:13 35151074 reads; of these: 35151074 (100.00%) were unpaired; of these: 1556914 (4.43%) aligned 0 times 21866827 (62.21%) aligned exactly 1 time 11727333 (33.36%) aligned >1 times 95.57% overall alignment rate Time searching: 00:14:14 Overall time: 00:14:14 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 16 files... [bam_rmdupse_core] 6205883 / 33594160 = 0.1847 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 22:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.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 22:56:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:56:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:56:22: 1000000 INFO @ Mon, 29 Jun 2020 22:56:29: 2000000 INFO @ Mon, 29 Jun 2020 22:56:35: 3000000 INFO @ Mon, 29 Jun 2020 22:56:41: 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 22:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.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 22:56:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:56:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:56:48: 5000000 INFO @ Mon, 29 Jun 2020 22:56:52: 1000000 INFO @ Mon, 29 Jun 2020 22:56:55: 6000000 INFO @ Mon, 29 Jun 2020 22:56:59: 2000000 INFO @ Mon, 29 Jun 2020 22:57:02: 7000000 INFO @ Mon, 29 Jun 2020 22:57:05: 3000000 INFO @ Mon, 29 Jun 2020 22:57:09: 8000000 INFO @ Mon, 29 Jun 2020 22:57:12: 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 22:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.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 22:57:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:57:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:57:16: 9000000 INFO @ Mon, 29 Jun 2020 22:57:19: 5000000 INFO @ Mon, 29 Jun 2020 22:57:22: 1000000 INFO @ Mon, 29 Jun 2020 22:57:23: 10000000 INFO @ Mon, 29 Jun 2020 22:57:26: 6000000 INFO @ Mon, 29 Jun 2020 22:57:28: 2000000 INFO @ Mon, 29 Jun 2020 22:57:30: 11000000 INFO @ Mon, 29 Jun 2020 22:57:33: 7000000 INFO @ Mon, 29 Jun 2020 22:57:34: 3000000 INFO @ Mon, 29 Jun 2020 22:57:37: 12000000 INFO @ Mon, 29 Jun 2020 22:57:40: 8000000 INFO @ Mon, 29 Jun 2020 22:57:41: 4000000 INFO @ Mon, 29 Jun 2020 22:57:44: 13000000 INFO @ Mon, 29 Jun 2020 22:57:47: 9000000 INFO @ Mon, 29 Jun 2020 22:57:47: 5000000 INFO @ Mon, 29 Jun 2020 22:57:51: 14000000 INFO @ Mon, 29 Jun 2020 22:57:54: 6000000 INFO @ Mon, 29 Jun 2020 22:57:54: 10000000 INFO @ Mon, 29 Jun 2020 22:57:58: 15000000 INFO @ Mon, 29 Jun 2020 22:58:00: 7000000 INFO @ Mon, 29 Jun 2020 22:58:01: 11000000 INFO @ Mon, 29 Jun 2020 22:58:04: 16000000 INFO @ Mon, 29 Jun 2020 22:58:07: 8000000 INFO @ Mon, 29 Jun 2020 22:58:07: 12000000 INFO @ Mon, 29 Jun 2020 22:58:11: 17000000 INFO @ Mon, 29 Jun 2020 22:58:13: 9000000 INFO @ Mon, 29 Jun 2020 22:58:14: 13000000 INFO @ Mon, 29 Jun 2020 22:58:18: 18000000 INFO @ Mon, 29 Jun 2020 22:58:20: 10000000 INFO @ Mon, 29 Jun 2020 22:58:21: 14000000 INFO @ Mon, 29 Jun 2020 22:58:25: 19000000 INFO @ Mon, 29 Jun 2020 22:58:26: 11000000 INFO @ Mon, 29 Jun 2020 22:58:28: 15000000 INFO @ Mon, 29 Jun 2020 22:58:32: 20000000 INFO @ Mon, 29 Jun 2020 22:58:32: 12000000 INFO @ Mon, 29 Jun 2020 22:58:35: 16000000 INFO @ Mon, 29 Jun 2020 22:58:39: 13000000 INFO @ Mon, 29 Jun 2020 22:58:39: 21000000 INFO @ Mon, 29 Jun 2020 22:58:42: 17000000 INFO @ Mon, 29 Jun 2020 22:58:45: 14000000 INFO @ Mon, 29 Jun 2020 22:58:46: 22000000 INFO @ Mon, 29 Jun 2020 22:58:49: 18000000 INFO @ Mon, 29 Jun 2020 22:58:51: 15000000 INFO @ Mon, 29 Jun 2020 22:58:53: 23000000 INFO @ Mon, 29 Jun 2020 22:58:56: 19000000 INFO @ Mon, 29 Jun 2020 22:58:58: 16000000 INFO @ Mon, 29 Jun 2020 22:59:00: 24000000 INFO @ Mon, 29 Jun 2020 22:59:02: 20000000 INFO @ Mon, 29 Jun 2020 22:59:04: 17000000 INFO @ Mon, 29 Jun 2020 22:59:07: 25000000 INFO @ Mon, 29 Jun 2020 22:59:09: 21000000 INFO @ Mon, 29 Jun 2020 22:59:10: 18000000 INFO @ Mon, 29 Jun 2020 22:59:14: 26000000 INFO @ Mon, 29 Jun 2020 22:59:16: 22000000 INFO @ Mon, 29 Jun 2020 22:59:17: 19000000 INFO @ Mon, 29 Jun 2020 22:59:21: 27000000 INFO @ Mon, 29 Jun 2020 22:59:23: 23000000 INFO @ Mon, 29 Jun 2020 22:59:23: 20000000 INFO @ Mon, 29 Jun 2020 22:59:24: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:59:24: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:59:24: #1 total tags in treatment: 27388277 INFO @ Mon, 29 Jun 2020 22:59:24: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:24: #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 22:59:24: #1 tags after filtering in treatment: 27388277 INFO @ Mon, 29 Jun 2020 22:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:24: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:24: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:26: #2 number of paired peaks: 251 WARNING @ Mon, 29 Jun 2020 22:59:26: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Mon, 29 Jun 2020 22:59:26: start model_add_line... INFO @ Mon, 29 Jun 2020 22:59:26: start X-correlation... INFO @ Mon, 29 Jun 2020 22:59:26: end of X-cor INFO @ Mon, 29 Jun 2020 22:59:26: #2 finished! INFO @ Mon, 29 Jun 2020 22:59:26: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 22:59:26: #2 alternative fragment length(s) may be 2,48,518,563 bps INFO @ Mon, 29 Jun 2020 22:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.05_model.r WARNING @ Mon, 29 Jun 2020 22:59:27: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:59:27: #2 You may need to consider one of the other alternative d(s): 2,48,518,563 WARNING @ Mon, 29 Jun 2020 22:59:27: #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 22:59:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:59:29: 24000000 INFO @ Mon, 29 Jun 2020 22:59:30: 21000000 INFO @ Mon, 29 Jun 2020 22:59:35: 25000000 INFO @ Mon, 29 Jun 2020 22:59:36: 22000000 INFO @ Mon, 29 Jun 2020 22:59:42: 26000000 INFO @ Mon, 29 Jun 2020 22:59:42: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:59:48: 27000000 INFO @ Mon, 29 Jun 2020 22:59:49: 24000000 INFO @ Mon, 29 Jun 2020 22:59:51: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:59:51: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:59:51: #1 total tags in treatment: 27388277 INFO @ Mon, 29 Jun 2020 22:59:51: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:51: #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 22:59:51: #1 tags after filtering in treatment: 27388277 INFO @ Mon, 29 Jun 2020 22:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:51: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:51: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:53: #2 number of paired peaks: 251 WARNING @ Mon, 29 Jun 2020 22:59:53: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Mon, 29 Jun 2020 22:59:53: start model_add_line... INFO @ Mon, 29 Jun 2020 22:59:53: start X-correlation... INFO @ Mon, 29 Jun 2020 22:59:53: end of X-cor INFO @ Mon, 29 Jun 2020 22:59:53: #2 finished! INFO @ Mon, 29 Jun 2020 22:59:53: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 22:59:53: #2 alternative fragment length(s) may be 2,48,518,563 bps INFO @ Mon, 29 Jun 2020 22:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.10_model.r WARNING @ Mon, 29 Jun 2020 22:59:54: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:59:54: #2 You may need to consider one of the other alternative d(s): 2,48,518,563 WARNING @ Mon, 29 Jun 2020 22:59:54: #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 22:59:54: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:59:55: 25000000 INFO @ Mon, 29 Jun 2020 23:00:01: 26000000 INFO @ Mon, 29 Jun 2020 23:00:08: 27000000 INFO @ Mon, 29 Jun 2020 23:00:10: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:00:10: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:00:10: #1 total tags in treatment: 27388277 INFO @ Mon, 29 Jun 2020 23:00:11: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:00:11: #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 23:00:11: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:00:11: #1 tags after filtering in treatment: 27388277 INFO @ Mon, 29 Jun 2020 23:00:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:00:11: #1 finished! INFO @ Mon, 29 Jun 2020 23:00:11: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:00:13: #2 number of paired peaks: 251 WARNING @ Mon, 29 Jun 2020 23:00:13: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Mon, 29 Jun 2020 23:00:13: start model_add_line... INFO @ Mon, 29 Jun 2020 23:00:13: start X-correlation... INFO @ Mon, 29 Jun 2020 23:00:13: end of X-cor INFO @ Mon, 29 Jun 2020 23:00:13: #2 finished! INFO @ Mon, 29 Jun 2020 23:00:13: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 23:00:13: #2 alternative fragment length(s) may be 2,48,518,563 bps INFO @ Mon, 29 Jun 2020 23:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.20_model.r WARNING @ Mon, 29 Jun 2020 23:00:14: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:00:14: #2 You may need to consider one of the other alternative d(s): 2,48,518,563 WARNING @ Mon, 29 Jun 2020 23:00:14: #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 23:00:14: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.05_summits.bed INFO @ Mon, 29 Jun 2020 23:00:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4003 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:00:38: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:00:57: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:01:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.10_summits.bed INFO @ Mon, 29 Jun 2020 23:01:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2819 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193328/SRX193328.20_summits.bed INFO @ Mon, 29 Jun 2020 23:01:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1618 records, 4 fields): 602 millis CompletedMACS2peakCalling