Job ID = 6458843 SRX = SRX5661489 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:37:14 prefetch.2.10.7: 1) Downloading 'SRR8874496'... 2020-06-21T12:37:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:41:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:41:44 prefetch.2.10.7: 1) 'SRR8874496' was downloaded successfully 2020-06-21T12:41:44 prefetch.2.10.7: 'SRR8874496' has 0 unresolved dependencies Read 35161197 spots for SRR8874496/SRR8874496.sra Written 35161197 spots for SRR8874496/SRR8874496.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: 00:10:00 35161197 reads; of these: 35161197 (100.00%) were unpaired; of these: 1104784 (3.14%) aligned 0 times 21784966 (61.96%) aligned exactly 1 time 12271447 (34.90%) aligned >1 times 96.86% overall alignment rate Time searching: 00:10:00 Overall time: 00:10:00 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] 9297821 / 34056413 = 0.2730 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 21:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.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 21:59:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:16: 1000000 INFO @ Sun, 21 Jun 2020 21:59:22: 2000000 INFO @ Sun, 21 Jun 2020 21:59:28: 3000000 INFO @ Sun, 21 Jun 2020 21:59:33: 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 21:59:39: 5000000 INFO @ Sun, 21 Jun 2020 21:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.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 21:59:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:45: 6000000 INFO @ Sun, 21 Jun 2020 21:59:48: 1000000 INFO @ Sun, 21 Jun 2020 21:59:52: 7000000 INFO @ Sun, 21 Jun 2020 21:59:56: 2000000 INFO @ Sun, 21 Jun 2020 21:59:59: 8000000 INFO @ Sun, 21 Jun 2020 22:00:03: 3000000 INFO @ Sun, 21 Jun 2020 22:00:06: 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 22:00:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.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 22:00:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:11: 4000000 INFO @ Sun, 21 Jun 2020 22:00:12: 10000000 INFO @ Sun, 21 Jun 2020 22:00:18: 1000000 INFO @ Sun, 21 Jun 2020 22:00:19: 5000000 INFO @ Sun, 21 Jun 2020 22:00:20: 11000000 INFO @ Sun, 21 Jun 2020 22:00:26: 2000000 INFO @ Sun, 21 Jun 2020 22:00:26: 6000000 INFO @ Sun, 21 Jun 2020 22:00:27: 12000000 INFO @ Sun, 21 Jun 2020 22:00:34: 13000000 INFO @ Sun, 21 Jun 2020 22:00:34: 7000000 INFO @ Sun, 21 Jun 2020 22:00:34: 3000000 INFO @ Sun, 21 Jun 2020 22:00:41: 14000000 INFO @ Sun, 21 Jun 2020 22:00:42: 8000000 INFO @ Sun, 21 Jun 2020 22:00:42: 4000000 INFO @ Sun, 21 Jun 2020 22:00:48: 15000000 INFO @ Sun, 21 Jun 2020 22:00:49: 9000000 INFO @ Sun, 21 Jun 2020 22:00:50: 5000000 INFO @ Sun, 21 Jun 2020 22:00:55: 16000000 INFO @ Sun, 21 Jun 2020 22:00:57: 10000000 INFO @ Sun, 21 Jun 2020 22:00:58: 6000000 INFO @ Sun, 21 Jun 2020 22:01:02: 17000000 INFO @ Sun, 21 Jun 2020 22:01:05: 11000000 INFO @ Sun, 21 Jun 2020 22:01:06: 7000000 INFO @ Sun, 21 Jun 2020 22:01:09: 18000000 INFO @ Sun, 21 Jun 2020 22:01:13: 12000000 INFO @ Sun, 21 Jun 2020 22:01:14: 8000000 INFO @ Sun, 21 Jun 2020 22:01:16: 19000000 INFO @ Sun, 21 Jun 2020 22:01:20: 13000000 INFO @ Sun, 21 Jun 2020 22:01:21: 9000000 INFO @ Sun, 21 Jun 2020 22:01:24: 20000000 INFO @ Sun, 21 Jun 2020 22:01:28: 14000000 INFO @ Sun, 21 Jun 2020 22:01:29: 10000000 INFO @ Sun, 21 Jun 2020 22:01:31: 21000000 INFO @ Sun, 21 Jun 2020 22:01:36: 15000000 INFO @ Sun, 21 Jun 2020 22:01:37: 11000000 INFO @ Sun, 21 Jun 2020 22:01:38: 22000000 INFO @ Sun, 21 Jun 2020 22:01:43: 16000000 INFO @ Sun, 21 Jun 2020 22:01:45: 23000000 INFO @ Sun, 21 Jun 2020 22:01:45: 12000000 INFO @ Sun, 21 Jun 2020 22:01:51: 17000000 INFO @ Sun, 21 Jun 2020 22:01:52: 24000000 INFO @ Sun, 21 Jun 2020 22:01:53: 13000000 INFO @ Sun, 21 Jun 2020 22:01:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:01:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:01:57: #1 total tags in treatment: 24758592 INFO @ Sun, 21 Jun 2020 22:01:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:57: #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 22:01:58: #1 tags after filtering in treatment: 24758535 INFO @ Sun, 21 Jun 2020 22:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:58: 18000000 INFO @ Sun, 21 Jun 2020 22:01:59: #2 number of paired peaks: 1030 INFO @ Sun, 21 Jun 2020 22:01:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:00: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:00: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:00: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:00: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:02:00: #2 alternative fragment length(s) may be 1,45 bps INFO @ Sun, 21 Jun 2020 22:02:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.05_model.r WARNING @ Sun, 21 Jun 2020 22:02:00: #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 22:02:00: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Sun, 21 Jun 2020 22:02:00: #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 22:02:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:01: 14000000 INFO @ Sun, 21 Jun 2020 22:02:06: 19000000 INFO @ Sun, 21 Jun 2020 22:02:08: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:13: 20000000 INFO @ Sun, 21 Jun 2020 22:02:16: 16000000 INFO @ Sun, 21 Jun 2020 22:02:20: 21000000 INFO @ Sun, 21 Jun 2020 22:02:23: 17000000 INFO @ Sun, 21 Jun 2020 22:02:28: 22000000 INFO @ Sun, 21 Jun 2020 22:02:30: 18000000 INFO @ Sun, 21 Jun 2020 22:02:35: 23000000 INFO @ Sun, 21 Jun 2020 22:02:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:38: 19000000 INFO @ Sun, 21 Jun 2020 22:02:42: 24000000 INFO @ Sun, 21 Jun 2020 22:02:45: 20000000 INFO @ Sun, 21 Jun 2020 22:02:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:02:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:02:47: #1 total tags in treatment: 24758592 INFO @ Sun, 21 Jun 2020 22:02:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:47: #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 22:02:48: #1 tags after filtering in treatment: 24758535 INFO @ Sun, 21 Jun 2020 22:02:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:48: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:50: #2 number of paired peaks: 1030 INFO @ Sun, 21 Jun 2020 22:02:50: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:50: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:50: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:50: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:50: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:02:50: #2 alternative fragment length(s) may be 1,45 bps INFO @ Sun, 21 Jun 2020 22:02:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.10_model.r WARNING @ Sun, 21 Jun 2020 22:02:50: #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 22:02:50: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Sun, 21 Jun 2020 22:02:50: #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 22:02:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:52: 21000000 INFO @ Sun, 21 Jun 2020 22:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.05_summits.bed INFO @ Sun, 21 Jun 2020 22:02:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:02:59: 22000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:03:06: 23000000 INFO @ Sun, 21 Jun 2020 22:03:13: 24000000 INFO @ Sun, 21 Jun 2020 22:03:18: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:03:18: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:03:18: #1 total tags in treatment: 24758592 INFO @ Sun, 21 Jun 2020 22:03:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:18: #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 22:03:18: #1 tags after filtering in treatment: 24758535 INFO @ Sun, 21 Jun 2020 22:03:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:18: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:20: #2 number of paired peaks: 1030 INFO @ Sun, 21 Jun 2020 22:03:20: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:20: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:20: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:20: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:20: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 22:03:20: #2 alternative fragment length(s) may be 1,45 bps INFO @ Sun, 21 Jun 2020 22:03:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.20_model.r WARNING @ Sun, 21 Jun 2020 22:03:20: #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 22:03:20: #2 You may need to consider one of the other alternative d(s): 1,45 WARNING @ Sun, 21 Jun 2020 22:03:20: #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 22:03:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:03:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:03:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:03:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:03:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.10_summits.bed INFO @ Sun, 21 Jun 2020 22:03:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:03:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661489/SRX5661489.20_summits.bed INFO @ Sun, 21 Jun 2020 22:04:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling