Job ID = 6458766 SRX = SRX5436040 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:34:07 prefetch.2.10.7: 1) Downloading 'SRR8637372'... 2020-06-21T12:34:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:38:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:38:09 prefetch.2.10.7: 1) 'SRR8637372' was downloaded successfully Read 36010157 spots for SRR8637372/SRR8637372.sra Written 36010157 spots for SRR8637372/SRR8637372.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: 00:10:38 36010157 reads; of these: 36010157 (100.00%) were unpaired; of these: 1425968 (3.96%) aligned 0 times 23696694 (65.81%) aligned exactly 1 time 10887495 (30.23%) aligned >1 times 96.04% overall alignment rate Time searching: 00:10:38 Overall time: 00:10:38 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 16 files... [bam_rmdupse_core] 6699961 / 34584189 = 0.1937 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 21:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.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 21:59:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:58: 1000000 INFO @ Sun, 21 Jun 2020 22:00:04: 2000000 INFO @ Sun, 21 Jun 2020 22:00:11: 3000000 INFO @ Sun, 21 Jun 2020 22:00:17: 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 22:00:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.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 22:00:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:24: 5000000 INFO @ Sun, 21 Jun 2020 22:00:28: 1000000 INFO @ Sun, 21 Jun 2020 22:00:30: 6000000 INFO @ Sun, 21 Jun 2020 22:00:35: 2000000 INFO @ Sun, 21 Jun 2020 22:00:37: 7000000 INFO @ Sun, 21 Jun 2020 22:00:41: 3000000 INFO @ Sun, 21 Jun 2020 22:00:44: 8000000 INFO @ Sun, 21 Jun 2020 22:00:48: 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 @ Sun, 21 Jun 2020 22:00:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.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 22:00:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:51: 9000000 INFO @ Sun, 21 Jun 2020 22:00:55: 5000000 INFO @ Sun, 21 Jun 2020 22:00:58: 10000000 INFO @ Sun, 21 Jun 2020 22:00:59: 1000000 INFO @ Sun, 21 Jun 2020 22:01:02: 6000000 INFO @ Sun, 21 Jun 2020 22:01:05: 11000000 INFO @ Sun, 21 Jun 2020 22:01:07: 2000000 INFO @ Sun, 21 Jun 2020 22:01:09: 7000000 INFO @ Sun, 21 Jun 2020 22:01:12: 12000000 INFO @ Sun, 21 Jun 2020 22:01:15: 3000000 INFO @ Sun, 21 Jun 2020 22:01:16: 8000000 INFO @ Sun, 21 Jun 2020 22:01:19: 13000000 INFO @ Sun, 21 Jun 2020 22:01:22: 4000000 INFO @ Sun, 21 Jun 2020 22:01:23: 9000000 INFO @ Sun, 21 Jun 2020 22:01:26: 14000000 INFO @ Sun, 21 Jun 2020 22:01:29: 10000000 INFO @ Sun, 21 Jun 2020 22:01:30: 5000000 INFO @ Sun, 21 Jun 2020 22:01:33: 15000000 INFO @ Sun, 21 Jun 2020 22:01:36: 11000000 INFO @ Sun, 21 Jun 2020 22:01:38: 6000000 INFO @ Sun, 21 Jun 2020 22:01:39: 16000000 INFO @ Sun, 21 Jun 2020 22:01:43: 12000000 INFO @ Sun, 21 Jun 2020 22:01:46: 7000000 INFO @ Sun, 21 Jun 2020 22:01:46: 17000000 INFO @ Sun, 21 Jun 2020 22:01:50: 13000000 INFO @ Sun, 21 Jun 2020 22:01:53: 18000000 INFO @ Sun, 21 Jun 2020 22:01:54: 8000000 INFO @ Sun, 21 Jun 2020 22:01:56: 14000000 INFO @ Sun, 21 Jun 2020 22:02:00: 19000000 INFO @ Sun, 21 Jun 2020 22:02:02: 9000000 INFO @ Sun, 21 Jun 2020 22:02:03: 15000000 INFO @ Sun, 21 Jun 2020 22:02:06: 20000000 INFO @ Sun, 21 Jun 2020 22:02:09: 16000000 INFO @ Sun, 21 Jun 2020 22:02:10: 10000000 INFO @ Sun, 21 Jun 2020 22:02:13: 21000000 INFO @ Sun, 21 Jun 2020 22:02:16: 17000000 INFO @ Sun, 21 Jun 2020 22:02:18: 11000000 INFO @ Sun, 21 Jun 2020 22:02:20: 22000000 INFO @ Sun, 21 Jun 2020 22:02:23: 18000000 INFO @ Sun, 21 Jun 2020 22:02:25: 12000000 INFO @ Sun, 21 Jun 2020 22:02:27: 23000000 INFO @ Sun, 21 Jun 2020 22:02:29: 19000000 INFO @ Sun, 21 Jun 2020 22:02:33: 13000000 INFO @ Sun, 21 Jun 2020 22:02:34: 24000000 INFO @ Sun, 21 Jun 2020 22:02:36: 20000000 INFO @ Sun, 21 Jun 2020 22:02:41: 14000000 INFO @ Sun, 21 Jun 2020 22:02:41: 25000000 INFO @ Sun, 21 Jun 2020 22:02:43: 21000000 INFO @ Sun, 21 Jun 2020 22:02:48: 26000000 INFO @ Sun, 21 Jun 2020 22:02:48: 15000000 INFO @ Sun, 21 Jun 2020 22:02:49: 22000000 INFO @ Sun, 21 Jun 2020 22:02:55: 27000000 INFO @ Sun, 21 Jun 2020 22:02:56: 16000000 INFO @ Sun, 21 Jun 2020 22:02:57: 23000000 INFO @ Sun, 21 Jun 2020 22:03:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:03:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:03:01: #1 total tags in treatment: 27884228 INFO @ Sun, 21 Jun 2020 22:03:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:01: #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 22:03:02: #1 tags after filtering in treatment: 27884174 INFO @ Sun, 21 Jun 2020 22:03:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:02: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:04: 24000000 INFO @ Sun, 21 Jun 2020 22:03:04: 17000000 INFO @ Sun, 21 Jun 2020 22:03:04: #2 number of paired peaks: 1184 INFO @ Sun, 21 Jun 2020 22:03:04: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:04: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:04: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:04: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:04: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:03:04: #2 alternative fragment length(s) may be 1,21 bps INFO @ Sun, 21 Jun 2020 22:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.05_model.r WARNING @ Sun, 21 Jun 2020 22:03:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:03:04: #2 You may need to consider one of the other alternative d(s): 1,21 WARNING @ Sun, 21 Jun 2020 22:03:04: #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 22:03:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:03:10: 25000000 INFO @ Sun, 21 Jun 2020 22:03:11: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:03:16: 26000000 INFO @ Sun, 21 Jun 2020 22:03:19: 19000000 INFO @ Sun, 21 Jun 2020 22:03:22: 27000000 INFO @ Sun, 21 Jun 2020 22:03:27: 20000000 INFO @ Sun, 21 Jun 2020 22:03:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:03:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:03:28: #1 total tags in treatment: 27884228 INFO @ Sun, 21 Jun 2020 22:03:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:28: #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 22:03:29: #1 tags after filtering in treatment: 27884174 INFO @ Sun, 21 Jun 2020 22:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:29: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:31: #2 number of paired peaks: 1184 INFO @ Sun, 21 Jun 2020 22:03:31: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:31: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:31: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:31: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:31: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:03:31: #2 alternative fragment length(s) may be 1,21 bps INFO @ Sun, 21 Jun 2020 22:03:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.10_model.r WARNING @ Sun, 21 Jun 2020 22:03:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:03:31: #2 You may need to consider one of the other alternative d(s): 1,21 WARNING @ Sun, 21 Jun 2020 22:03:31: #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 22:03:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:03:35: 21000000 INFO @ Sun, 21 Jun 2020 22:03:43: 22000000 INFO @ Sun, 21 Jun 2020 22:03:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:51: 23000000 INFO @ Sun, 21 Jun 2020 22:04:00: 24000000 INFO @ Sun, 21 Jun 2020 22:04:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.05_summits.bed INFO @ Sun, 21 Jun 2020 22:04:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:07: 25000000 INFO @ Sun, 21 Jun 2020 22:04:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:15: 26000000 INFO @ Sun, 21 Jun 2020 22:04:23: 27000000 INFO @ Sun, 21 Jun 2020 22:04:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:04:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:04:30: #1 total tags in treatment: 27884228 INFO @ Sun, 21 Jun 2020 22:04:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:30: #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 22:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.10_summits.bed INFO @ Sun, 21 Jun 2020 22:04:31: Done! INFO @ Sun, 21 Jun 2020 22:04:31: #1 tags after filtering in treatment: 27884174 INFO @ Sun, 21 Jun 2020 22:04:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:31: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:31: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:33: #2 number of paired peaks: 1184 INFO @ Sun, 21 Jun 2020 22:04:33: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:04:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:33: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:04:33: #2 alternative fragment length(s) may be 1,21 bps INFO @ Sun, 21 Jun 2020 22:04:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.20_model.r WARNING @ Sun, 21 Jun 2020 22:04:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:33: #2 You may need to consider one of the other alternative d(s): 1,21 WARNING @ Sun, 21 Jun 2020 22:04:33: #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 22:04:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436040/SRX5436040.20_summits.bed INFO @ Sun, 21 Jun 2020 22:05:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling