Job ID = 6527815 SRX = SRX287737 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:41:14 prefetch.2.10.7: 1) Downloading 'SRR869926'... 2020-06-29T13:41:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:43:28 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:43:28 prefetch.2.10.7: 1) 'SRR869926' was downloaded successfully Read 22382823 spots for SRR869926/SRR869926.sra Written 22382823 spots for SRR869926/SRR869926.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: 00:07:27 22382823 reads; of these: 22382823 (100.00%) were unpaired; of these: 1147737 (5.13%) aligned 0 times 14422353 (64.43%) aligned exactly 1 time 6812733 (30.44%) aligned >1 times 94.87% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 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] 4905559 / 21235086 = 0.2310 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 23:02:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.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 23:02:06: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:02:06: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:02:12: 1000000 INFO @ Mon, 29 Jun 2020 23:02:18: 2000000 INFO @ Mon, 29 Jun 2020 23:02:23: 3000000 INFO @ Mon, 29 Jun 2020 23:02:29: 4000000 INFO @ Mon, 29 Jun 2020 23:02:34: 5000000 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 23:02:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.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 23:02:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:02:36: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:02:40: 6000000 INFO @ Mon, 29 Jun 2020 23:02:43: 1000000 INFO @ Mon, 29 Jun 2020 23:02:47: 7000000 INFO @ Mon, 29 Jun 2020 23:02:49: 2000000 INFO @ Mon, 29 Jun 2020 23:02:53: 8000000 INFO @ Mon, 29 Jun 2020 23:02:56: 3000000 INFO @ Mon, 29 Jun 2020 23:02:59: 9000000 INFO @ Mon, 29 Jun 2020 23:03:02: 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 23:03:05: 10000000 INFO @ Mon, 29 Jun 2020 23:03:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.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 23:03:06: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:03:06: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:03:08: 5000000 INFO @ Mon, 29 Jun 2020 23:03:12: 11000000 INFO @ Mon, 29 Jun 2020 23:03:13: 1000000 INFO @ Mon, 29 Jun 2020 23:03:15: 6000000 INFO @ Mon, 29 Jun 2020 23:03:18: 12000000 INFO @ Mon, 29 Jun 2020 23:03:19: 2000000 INFO @ Mon, 29 Jun 2020 23:03:21: 7000000 INFO @ Mon, 29 Jun 2020 23:03:24: 13000000 INFO @ Mon, 29 Jun 2020 23:03:26: 3000000 INFO @ Mon, 29 Jun 2020 23:03:28: 8000000 INFO @ Mon, 29 Jun 2020 23:03:31: 14000000 INFO @ Mon, 29 Jun 2020 23:03:32: 4000000 INFO @ Mon, 29 Jun 2020 23:03:34: 9000000 INFO @ Mon, 29 Jun 2020 23:03:38: 15000000 INFO @ Mon, 29 Jun 2020 23:03:38: 5000000 INFO @ Mon, 29 Jun 2020 23:03:41: 10000000 INFO @ Mon, 29 Jun 2020 23:03:44: 16000000 INFO @ Mon, 29 Jun 2020 23:03:45: 6000000 INFO @ Mon, 29 Jun 2020 23:03:47: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:03:47: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:03:47: #1 total tags in treatment: 16329527 INFO @ Mon, 29 Jun 2020 23:03:47: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:03:47: #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 23:03:47: #1 tags after filtering in treatment: 16329527 INFO @ Mon, 29 Jun 2020 23:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:03:47: #1 finished! INFO @ Mon, 29 Jun 2020 23:03:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:03:47: 11000000 INFO @ Mon, 29 Jun 2020 23:03:48: #2 number of paired peaks: 217 WARNING @ Mon, 29 Jun 2020 23:03:48: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Mon, 29 Jun 2020 23:03:48: start model_add_line... INFO @ Mon, 29 Jun 2020 23:03:48: start X-correlation... INFO @ Mon, 29 Jun 2020 23:03:48: end of X-cor INFO @ Mon, 29 Jun 2020 23:03:48: #2 finished! INFO @ Mon, 29 Jun 2020 23:03:48: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:03:48: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:03:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.05_model.r WARNING @ Mon, 29 Jun 2020 23:03:48: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:03:48: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:03:48: #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 23:03:48: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:03:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:03:51: 7000000 INFO @ Mon, 29 Jun 2020 23:03:53: 12000000 INFO @ Mon, 29 Jun 2020 23:03:57: 8000000 INFO @ Mon, 29 Jun 2020 23:04:00: 13000000 INFO @ Mon, 29 Jun 2020 23:04:04: 9000000 INFO @ Mon, 29 Jun 2020 23:04:06: 14000000 INFO @ Mon, 29 Jun 2020 23:04:10: 10000000 INFO @ Mon, 29 Jun 2020 23:04:13: 15000000 INFO @ Mon, 29 Jun 2020 23:04:16: 11000000 INFO @ Mon, 29 Jun 2020 23:04:18: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:04:20: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:04:22: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:04:22: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:04:22: #1 total tags in treatment: 16329527 INFO @ Mon, 29 Jun 2020 23:04:22: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:04:22: #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 23:04:22: #1 tags after filtering in treatment: 16329527 INFO @ Mon, 29 Jun 2020 23:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:04:22: #1 finished! INFO @ Mon, 29 Jun 2020 23:04:22: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:04:22: 12000000 INFO @ Mon, 29 Jun 2020 23:04:23: #2 number of paired peaks: 217 WARNING @ Mon, 29 Jun 2020 23:04:23: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Mon, 29 Jun 2020 23:04:23: start model_add_line... INFO @ Mon, 29 Jun 2020 23:04:23: start X-correlation... INFO @ Mon, 29 Jun 2020 23:04:23: end of X-cor INFO @ Mon, 29 Jun 2020 23:04:23: #2 finished! INFO @ Mon, 29 Jun 2020 23:04:23: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:04:23: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.10_model.r WARNING @ Mon, 29 Jun 2020 23:04:23: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:04:23: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:04:23: #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 23:04:23: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:04:28: 13000000 INFO @ Mon, 29 Jun 2020 23:04:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:04:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:04:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.05_summits.bed INFO @ Mon, 29 Jun 2020 23:04:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2216 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:04:34: 14000000 INFO @ Mon, 29 Jun 2020 23:04:41: 15000000 INFO @ Mon, 29 Jun 2020 23:04:47: 16000000 INFO @ Mon, 29 Jun 2020 23:04:49: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:04:49: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:04:49: #1 total tags in treatment: 16329527 INFO @ Mon, 29 Jun 2020 23:04:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:04:49: #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 23:04:49: #1 tags after filtering in treatment: 16329527 INFO @ Mon, 29 Jun 2020 23:04:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:04:49: #1 finished! INFO @ Mon, 29 Jun 2020 23:04:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:04:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:04:50: #2 number of paired peaks: 217 WARNING @ Mon, 29 Jun 2020 23:04:50: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Mon, 29 Jun 2020 23:04:50: start model_add_line... INFO @ Mon, 29 Jun 2020 23:04:50: start X-correlation... INFO @ Mon, 29 Jun 2020 23:04:50: end of X-cor INFO @ Mon, 29 Jun 2020 23:04:50: #2 finished! INFO @ Mon, 29 Jun 2020 23:04:50: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:04:50: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:04:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.20_model.r WARNING @ Mon, 29 Jun 2020 23:04:50: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:04:50: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:04:50: #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 23:04:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:04:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:04:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.10_summits.bed INFO @ Mon, 29 Jun 2020 23:05:09: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1811 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:05:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:05:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287737/SRX287737.20_summits.bed INFO @ Mon, 29 Jun 2020 23:05:34: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1301 records, 4 fields): 3 millis CompletedMACS2peakCalling