Job ID = 6528099 SRX = SRX4664656 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:29:51 prefetch.2.10.7: 1) Downloading 'SRR7813083'... 2020-06-29T14:29:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:33:45 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:33:45 prefetch.2.10.7: 1) 'SRR7813083' was downloaded successfully Read 31909608 spots for SRR7813083/SRR7813083.sra Written 31909608 spots for SRR7813083/SRR7813083.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: 00:13:00 31909608 reads; of these: 31909608 (100.00%) were unpaired; of these: 756656 (2.37%) aligned 0 times 20885036 (65.45%) aligned exactly 1 time 10267916 (32.18%) aligned >1 times 97.63% overall alignment rate Time searching: 00:13:00 Overall time: 00:13:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 4867282 / 31152952 = 0.1562 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 @ Tue, 30 Jun 2020 00:01:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.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 @ Tue, 30 Jun 2020 00:01:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:01:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:02:00: 1000000 INFO @ Tue, 30 Jun 2020 00:02:06: 2000000 INFO @ Tue, 30 Jun 2020 00:02:11: 3000000 INFO @ Tue, 30 Jun 2020 00:02:17: 4000000 INFO @ Tue, 30 Jun 2020 00:02:22: 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 @ Tue, 30 Jun 2020 00:02:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.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 @ Tue, 30 Jun 2020 00:02:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:02:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:02:28: 6000000 INFO @ Tue, 30 Jun 2020 00:02:32: 1000000 INFO @ Tue, 30 Jun 2020 00:02:34: 7000000 INFO @ Tue, 30 Jun 2020 00:02:38: 2000000 INFO @ Tue, 30 Jun 2020 00:02:41: 8000000 INFO @ Tue, 30 Jun 2020 00:02:44: 3000000 INFO @ Tue, 30 Jun 2020 00:02:47: 9000000 INFO @ Tue, 30 Jun 2020 00:02:51: 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 @ Tue, 30 Jun 2020 00:02:53: 10000000 INFO @ Tue, 30 Jun 2020 00:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.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 @ Tue, 30 Jun 2020 00:02:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:02:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:02:57: 5000000 INFO @ Tue, 30 Jun 2020 00:03:00: 11000000 INFO @ Tue, 30 Jun 2020 00:03:03: 1000000 INFO @ Tue, 30 Jun 2020 00:03:04: 6000000 INFO @ Tue, 30 Jun 2020 00:03:06: 12000000 INFO @ Tue, 30 Jun 2020 00:03:09: 2000000 INFO @ Tue, 30 Jun 2020 00:03:10: 7000000 INFO @ Tue, 30 Jun 2020 00:03:13: 13000000 INFO @ Tue, 30 Jun 2020 00:03:16: 3000000 INFO @ Tue, 30 Jun 2020 00:03:16: 8000000 INFO @ Tue, 30 Jun 2020 00:03:19: 14000000 INFO @ Tue, 30 Jun 2020 00:03:22: 4000000 INFO @ Tue, 30 Jun 2020 00:03:23: 9000000 INFO @ Tue, 30 Jun 2020 00:03:25: 15000000 INFO @ Tue, 30 Jun 2020 00:03:29: 5000000 INFO @ Tue, 30 Jun 2020 00:03:29: 10000000 INFO @ Tue, 30 Jun 2020 00:03:32: 16000000 INFO @ Tue, 30 Jun 2020 00:03:35: 6000000 INFO @ Tue, 30 Jun 2020 00:03:36: 11000000 INFO @ Tue, 30 Jun 2020 00:03:38: 17000000 INFO @ Tue, 30 Jun 2020 00:03:42: 7000000 INFO @ Tue, 30 Jun 2020 00:03:42: 12000000 INFO @ Tue, 30 Jun 2020 00:03:45: 18000000 INFO @ Tue, 30 Jun 2020 00:03:48: 8000000 INFO @ Tue, 30 Jun 2020 00:03:49: 13000000 INFO @ Tue, 30 Jun 2020 00:03:51: 19000000 INFO @ Tue, 30 Jun 2020 00:03:55: 9000000 INFO @ Tue, 30 Jun 2020 00:03:55: 14000000 INFO @ Tue, 30 Jun 2020 00:03:58: 20000000 INFO @ Tue, 30 Jun 2020 00:04:01: 10000000 INFO @ Tue, 30 Jun 2020 00:04:02: 15000000 INFO @ Tue, 30 Jun 2020 00:04:04: 21000000 INFO @ Tue, 30 Jun 2020 00:04:08: 11000000 INFO @ Tue, 30 Jun 2020 00:04:08: 16000000 INFO @ Tue, 30 Jun 2020 00:04:10: 22000000 INFO @ Tue, 30 Jun 2020 00:04:14: 12000000 INFO @ Tue, 30 Jun 2020 00:04:15: 17000000 INFO @ Tue, 30 Jun 2020 00:04:17: 23000000 INFO @ Tue, 30 Jun 2020 00:04:21: 13000000 INFO @ Tue, 30 Jun 2020 00:04:21: 18000000 INFO @ Tue, 30 Jun 2020 00:04:23: 24000000 INFO @ Tue, 30 Jun 2020 00:04:27: 14000000 INFO @ Tue, 30 Jun 2020 00:04:28: 19000000 INFO @ Tue, 30 Jun 2020 00:04:30: 25000000 INFO @ Tue, 30 Jun 2020 00:04:34: 15000000 INFO @ Tue, 30 Jun 2020 00:04:34: 20000000 INFO @ Tue, 30 Jun 2020 00:04:36: 26000000 INFO @ Tue, 30 Jun 2020 00:04:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:04:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:04:38: #1 total tags in treatment: 26285670 INFO @ Tue, 30 Jun 2020 00:04:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:04:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:04:38: #1 tags after filtering in treatment: 26285670 INFO @ Tue, 30 Jun 2020 00:04:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:04:38: #1 finished! INFO @ Tue, 30 Jun 2020 00:04:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:04:40: 16000000 INFO @ Tue, 30 Jun 2020 00:04:40: #2 number of paired peaks: 464 WARNING @ Tue, 30 Jun 2020 00:04:40: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 30 Jun 2020 00:04:40: start model_add_line... INFO @ Tue, 30 Jun 2020 00:04:40: start X-correlation... INFO @ Tue, 30 Jun 2020 00:04:40: end of X-cor INFO @ Tue, 30 Jun 2020 00:04:40: #2 finished! INFO @ Tue, 30 Jun 2020 00:04:40: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:04:40: #2 alternative fragment length(s) may be 2,15,24 bps INFO @ Tue, 30 Jun 2020 00:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.05_model.r WARNING @ Tue, 30 Jun 2020 00:04:40: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:04:40: #2 You may need to consider one of the other alternative d(s): 2,15,24 WARNING @ Tue, 30 Jun 2020 00:04:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:04:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:04:41: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:04:46: 17000000 INFO @ Tue, 30 Jun 2020 00:04:47: 22000000 INFO @ Tue, 30 Jun 2020 00:04:53: 18000000 INFO @ Tue, 30 Jun 2020 00:04:54: 23000000 INFO @ Tue, 30 Jun 2020 00:04:59: 19000000 INFO @ Tue, 30 Jun 2020 00:05:00: 24000000 INFO @ Tue, 30 Jun 2020 00:05:05: 20000000 INFO @ Tue, 30 Jun 2020 00:05:06: 25000000 INFO @ Tue, 30 Jun 2020 00:05:12: 21000000 INFO @ Tue, 30 Jun 2020 00:05:13: 26000000 INFO @ Tue, 30 Jun 2020 00:05:14: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:05:14: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:05:14: #1 total tags in treatment: 26285670 INFO @ Tue, 30 Jun 2020 00:05:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:05:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:05:15: #1 tags after filtering in treatment: 26285670 INFO @ Tue, 30 Jun 2020 00:05:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:05:15: #1 finished! INFO @ Tue, 30 Jun 2020 00:05:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:05:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:05:17: #2 number of paired peaks: 464 WARNING @ Tue, 30 Jun 2020 00:05:17: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 30 Jun 2020 00:05:17: start model_add_line... INFO @ Tue, 30 Jun 2020 00:05:17: start X-correlation... INFO @ Tue, 30 Jun 2020 00:05:17: end of X-cor INFO @ Tue, 30 Jun 2020 00:05:17: #2 finished! INFO @ Tue, 30 Jun 2020 00:05:17: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:05:17: #2 alternative fragment length(s) may be 2,15,24 bps INFO @ Tue, 30 Jun 2020 00:05:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.10_model.r WARNING @ Tue, 30 Jun 2020 00:05:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:05:17: #2 You may need to consider one of the other alternative d(s): 2,15,24 WARNING @ Tue, 30 Jun 2020 00:05:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:05:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:05:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:05:18: 22000000 INFO @ Tue, 30 Jun 2020 00:05:23: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:05:24: 23000000 INFO @ Tue, 30 Jun 2020 00:05:29: 24000000 INFO @ Tue, 30 Jun 2020 00:05:35: 25000000 INFO @ Tue, 30 Jun 2020 00:05:41: 26000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:05:43: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:05:43: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:05:43: #1 total tags in treatment: 26285670 INFO @ Tue, 30 Jun 2020 00:05:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:05:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:05:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:05:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:05:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.05_summits.bed INFO @ Tue, 30 Jun 2020 00:05:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:05:43: #1 tags after filtering in treatment: 26285670 INFO @ Tue, 30 Jun 2020 00:05:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:05:43: #1 finished! INFO @ Tue, 30 Jun 2020 00:05:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:05:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:05:45: #2 number of paired peaks: 464 WARNING @ Tue, 30 Jun 2020 00:05:45: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Tue, 30 Jun 2020 00:05:45: start model_add_line... INFO @ Tue, 30 Jun 2020 00:05:45: start X-correlation... INFO @ Tue, 30 Jun 2020 00:05:45: end of X-cor INFO @ Tue, 30 Jun 2020 00:05:45: #2 finished! INFO @ Tue, 30 Jun 2020 00:05:45: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 00:05:45: #2 alternative fragment length(s) may be 2,15,24 bps INFO @ Tue, 30 Jun 2020 00:05:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.20_model.r WARNING @ Tue, 30 Jun 2020 00:05:45: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:05:45: #2 You may need to consider one of the other alternative d(s): 2,15,24 WARNING @ Tue, 30 Jun 2020 00:05:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:05:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:05:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:05:57: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:06:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:06:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:06:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.10_summits.bed INFO @ Tue, 30 Jun 2020 00:06:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:06:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664656/SRX4664656.20_summits.bed INFO @ Tue, 30 Jun 2020 00:06:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling