Job ID = 6454439 SRX = SRX2055967 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:21:29 prefetch.2.10.7: 1) Downloading 'SRR4069199'... 2020-06-21T09:21:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:31:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:31:47 prefetch.2.10.7: 1) 'SRR4069199' was downloaded successfully Read 26225419 spots for SRR4069199/SRR4069199.sra Written 26225419 spots for SRR4069199/SRR4069199.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: 00:08:37 26225419 reads; of these: 26225419 (100.00%) were unpaired; of these: 2872126 (10.95%) aligned 0 times 16106125 (61.41%) aligned exactly 1 time 7247168 (27.63%) aligned >1 times 89.05% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 3208572 / 23353293 = 0.1374 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 18:47:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.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 18:47:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:47:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:47:36: 1000000 INFO @ Sun, 21 Jun 2020 18:47:42: 2000000 INFO @ Sun, 21 Jun 2020 18:47:48: 3000000 INFO @ Sun, 21 Jun 2020 18:47:54: 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 18:48:00: 5000000 INFO @ Sun, 21 Jun 2020 18:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.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 18:48:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:06: 6000000 INFO @ Sun, 21 Jun 2020 18:48:10: 1000000 INFO @ Sun, 21 Jun 2020 18:48:13: 7000000 INFO @ Sun, 21 Jun 2020 18:48:17: 2000000 INFO @ Sun, 21 Jun 2020 18:48:19: 8000000 INFO @ Sun, 21 Jun 2020 18:48:23: 3000000 INFO @ Sun, 21 Jun 2020 18:48:26: 9000000 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 18:48:30: 4000000 INFO @ Sun, 21 Jun 2020 18:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.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 18:48:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:48:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:48:32: 10000000 INFO @ Sun, 21 Jun 2020 18:48:36: 5000000 INFO @ Sun, 21 Jun 2020 18:48:37: 1000000 INFO @ Sun, 21 Jun 2020 18:48:39: 11000000 INFO @ Sun, 21 Jun 2020 18:48:43: 6000000 INFO @ Sun, 21 Jun 2020 18:48:44: 2000000 INFO @ Sun, 21 Jun 2020 18:48:45: 12000000 INFO @ Sun, 21 Jun 2020 18:48:49: 7000000 INFO @ Sun, 21 Jun 2020 18:48:51: 3000000 INFO @ Sun, 21 Jun 2020 18:48:52: 13000000 INFO @ Sun, 21 Jun 2020 18:48:56: 8000000 INFO @ Sun, 21 Jun 2020 18:48:58: 4000000 INFO @ Sun, 21 Jun 2020 18:48:58: 14000000 INFO @ Sun, 21 Jun 2020 18:49:03: 9000000 INFO @ Sun, 21 Jun 2020 18:49:05: 15000000 INFO @ Sun, 21 Jun 2020 18:49:05: 5000000 INFO @ Sun, 21 Jun 2020 18:49:10: 10000000 INFO @ Sun, 21 Jun 2020 18:49:11: 16000000 INFO @ Sun, 21 Jun 2020 18:49:12: 6000000 INFO @ Sun, 21 Jun 2020 18:49:17: 11000000 INFO @ Sun, 21 Jun 2020 18:49:18: 17000000 INFO @ Sun, 21 Jun 2020 18:49:19: 7000000 INFO @ Sun, 21 Jun 2020 18:49:23: 12000000 INFO @ Sun, 21 Jun 2020 18:49:25: 18000000 INFO @ Sun, 21 Jun 2020 18:49:25: 8000000 INFO @ Sun, 21 Jun 2020 18:49:30: 13000000 INFO @ Sun, 21 Jun 2020 18:49:31: 19000000 INFO @ Sun, 21 Jun 2020 18:49:32: 9000000 INFO @ Sun, 21 Jun 2020 18:49:37: 14000000 INFO @ Sun, 21 Jun 2020 18:49:38: 20000000 INFO @ Sun, 21 Jun 2020 18:49:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:49:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:49:39: #1 total tags in treatment: 20144721 INFO @ Sun, 21 Jun 2020 18:49:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:49:39: #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 18:49:39: 10000000 INFO @ Sun, 21 Jun 2020 18:49:39: #1 tags after filtering in treatment: 20144654 INFO @ Sun, 21 Jun 2020 18:49:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:49:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:49:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:49:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:49:41: #2 number of paired peaks: 1176 INFO @ Sun, 21 Jun 2020 18:49:41: start model_add_line... INFO @ Sun, 21 Jun 2020 18:49:41: start X-correlation... INFO @ Sun, 21 Jun 2020 18:49:41: end of X-cor INFO @ Sun, 21 Jun 2020 18:49:41: #2 finished! INFO @ Sun, 21 Jun 2020 18:49:41: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:49:41: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:49:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.05_model.r WARNING @ Sun, 21 Jun 2020 18:49:41: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:49:41: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:49:41: #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 18:49:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:49:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:49:43: 15000000 INFO @ Sun, 21 Jun 2020 18:49:46: 11000000 INFO @ Sun, 21 Jun 2020 18:49:50: 16000000 INFO @ Sun, 21 Jun 2020 18:49:53: 12000000 INFO @ Sun, 21 Jun 2020 18:49:57: 17000000 INFO @ Sun, 21 Jun 2020 18:49:59: 13000000 INFO @ Sun, 21 Jun 2020 18:50:03: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:50:06: 14000000 INFO @ Sun, 21 Jun 2020 18:50:10: 19000000 INFO @ Sun, 21 Jun 2020 18:50:13: 15000000 INFO @ Sun, 21 Jun 2020 18:50:16: 20000000 INFO @ Sun, 21 Jun 2020 18:50:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:50:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:50:17: #1 total tags in treatment: 20144721 INFO @ Sun, 21 Jun 2020 18:50:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:17: #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 18:50:18: #1 tags after filtering in treatment: 20144654 INFO @ Sun, 21 Jun 2020 18:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:18: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:19: 16000000 INFO @ Sun, 21 Jun 2020 18:50:20: #2 number of paired peaks: 1176 INFO @ Sun, 21 Jun 2020 18:50:20: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:20: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:20: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:20: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:20: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:50:20: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.10_model.r WARNING @ Sun, 21 Jun 2020 18:50:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:20: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:50:20: #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 18:50:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:50:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:50:26: 17000000 INFO @ Sun, 21 Jun 2020 18:50:32: 18000000 INFO @ Sun, 21 Jun 2020 18:50:38: 19000000 INFO @ Sun, 21 Jun 2020 18:50:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:50:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:50:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.05_summits.bed INFO @ Sun, 21 Jun 2020 18:50:41: Done! pass1 - making usageList (668 chroms): 1 millis pass2 - checking and writing primary data (3464 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:50:44: 20000000 INFO @ Sun, 21 Jun 2020 18:50:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:50:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:50:45: #1 total tags in treatment: 20144721 INFO @ Sun, 21 Jun 2020 18:50:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:50:45: #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 18:50:46: #1 tags after filtering in treatment: 20144654 INFO @ Sun, 21 Jun 2020 18:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:50:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:50:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:50:47: #2 number of paired peaks: 1176 INFO @ Sun, 21 Jun 2020 18:50:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:50:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:50:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:50:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:50:48: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 18:50:48: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 18:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.20_model.r WARNING @ Sun, 21 Jun 2020 18:50:48: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:50:48: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 18:50:48: #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 18:50:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:50:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:50:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.10_summits.bed INFO @ Sun, 21 Jun 2020 18:51:19: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (2342 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:51:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:51:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:51:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:51:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055967/SRX2055967.20_summits.bed INFO @ Sun, 21 Jun 2020 18:51:47: Done! pass1 - making usageList (412 chroms): 1 millis pass2 - checking and writing primary data (1124 records, 4 fields): 14 millis CompletedMACS2peakCalling