Job ID = 6527955 SRX = SRX3404020 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:02:51 prefetch.2.10.7: 1) Downloading 'SRR6303497'... 2020-06-29T14:02:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:04:58 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:04:59 prefetch.2.10.7: 'SRR6303497' is valid 2020-06-29T14:04:59 prefetch.2.10.7: 1) 'SRR6303497' was downloaded successfully 2020-06-29T14:04:59 prefetch.2.10.7: 'SRR6303497' has 0 unresolved dependencies Read 26288689 spots for SRR6303497/SRR6303497.sra Written 26288689 spots for SRR6303497/SRR6303497.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: 00:08:24 26288689 reads; of these: 26288689 (100.00%) were unpaired; of these: 775267 (2.95%) aligned 0 times 18349560 (69.80%) aligned exactly 1 time 7163862 (27.25%) aligned >1 times 97.05% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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] 2044476 / 25513422 = 0.0801 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 23:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.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 23:25:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:25:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:26:00: 1000000 INFO @ Mon, 29 Jun 2020 23:26:05: 2000000 INFO @ Mon, 29 Jun 2020 23:26:10: 3000000 INFO @ Mon, 29 Jun 2020 23:26:14: 4000000 INFO @ Mon, 29 Jun 2020 23:26:19: 5000000 INFO @ Mon, 29 Jun 2020 23:26:23: 6000000 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 23:26:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.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 23:26:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:26:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:26:28: 7000000 INFO @ Mon, 29 Jun 2020 23:26:31: 1000000 INFO @ Mon, 29 Jun 2020 23:26:33: 8000000 INFO @ Mon, 29 Jun 2020 23:26:37: 2000000 INFO @ Mon, 29 Jun 2020 23:26:38: 9000000 INFO @ Mon, 29 Jun 2020 23:26:42: 3000000 INFO @ Mon, 29 Jun 2020 23:26:43: 10000000 INFO @ Mon, 29 Jun 2020 23:26:48: 11000000 INFO @ Mon, 29 Jun 2020 23:26:48: 4000000 INFO @ Mon, 29 Jun 2020 23:26:52: 12000000 INFO @ Mon, 29 Jun 2020 23:26:53: 5000000 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 23:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.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 23:26:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:26:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:26:57: 13000000 INFO @ Mon, 29 Jun 2020 23:26:59: 6000000 INFO @ Mon, 29 Jun 2020 23:27:01: 1000000 INFO @ Mon, 29 Jun 2020 23:27:02: 14000000 INFO @ Mon, 29 Jun 2020 23:27:04: 7000000 INFO @ Mon, 29 Jun 2020 23:27:06: 2000000 INFO @ Mon, 29 Jun 2020 23:27:07: 15000000 INFO @ Mon, 29 Jun 2020 23:27:10: 8000000 INFO @ Mon, 29 Jun 2020 23:27:11: 3000000 INFO @ Mon, 29 Jun 2020 23:27:12: 16000000 INFO @ Mon, 29 Jun 2020 23:27:15: 9000000 INFO @ Mon, 29 Jun 2020 23:27:16: 4000000 INFO @ Mon, 29 Jun 2020 23:27:17: 17000000 INFO @ Mon, 29 Jun 2020 23:27:21: 10000000 INFO @ Mon, 29 Jun 2020 23:27:21: 5000000 INFO @ Mon, 29 Jun 2020 23:27:22: 18000000 INFO @ Mon, 29 Jun 2020 23:27:26: 6000000 INFO @ Mon, 29 Jun 2020 23:27:26: 11000000 INFO @ Mon, 29 Jun 2020 23:27:27: 19000000 INFO @ Mon, 29 Jun 2020 23:27:31: 7000000 INFO @ Mon, 29 Jun 2020 23:27:32: 20000000 INFO @ Mon, 29 Jun 2020 23:27:32: 12000000 INFO @ Mon, 29 Jun 2020 23:27:37: 21000000 INFO @ Mon, 29 Jun 2020 23:27:37: 8000000 INFO @ Mon, 29 Jun 2020 23:27:37: 13000000 INFO @ Mon, 29 Jun 2020 23:27:42: 22000000 INFO @ Mon, 29 Jun 2020 23:27:42: 9000000 INFO @ Mon, 29 Jun 2020 23:27:43: 14000000 INFO @ Mon, 29 Jun 2020 23:27:47: 23000000 INFO @ Mon, 29 Jun 2020 23:27:47: 10000000 INFO @ Mon, 29 Jun 2020 23:27:48: 15000000 INFO @ Mon, 29 Jun 2020 23:27:49: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:27:49: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:27:49: #1 total tags in treatment: 23468946 INFO @ Mon, 29 Jun 2020 23:27:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:27:49: #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 23:27:50: #1 tags after filtering in treatment: 23468946 INFO @ Mon, 29 Jun 2020 23:27:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:27:50: #1 finished! INFO @ Mon, 29 Jun 2020 23:27:50: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:27:51: #2 number of paired peaks: 183 WARNING @ Mon, 29 Jun 2020 23:27:51: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Mon, 29 Jun 2020 23:27:51: start model_add_line... INFO @ Mon, 29 Jun 2020 23:27:51: start X-correlation... INFO @ Mon, 29 Jun 2020 23:27:51: end of X-cor INFO @ Mon, 29 Jun 2020 23:27:51: #2 finished! INFO @ Mon, 29 Jun 2020 23:27:51: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 23:27:51: #2 alternative fragment length(s) may be 1,46,575 bps INFO @ Mon, 29 Jun 2020 23:27:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.05_model.r WARNING @ Mon, 29 Jun 2020 23:27:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:27:51: #2 You may need to consider one of the other alternative d(s): 1,46,575 WARNING @ Mon, 29 Jun 2020 23:27:51: #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 23:27:51: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:27:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:27:52: 11000000 INFO @ Mon, 29 Jun 2020 23:27:54: 16000000 INFO @ Mon, 29 Jun 2020 23:27:57: 12000000 INFO @ Mon, 29 Jun 2020 23:27:59: 17000000 INFO @ Mon, 29 Jun 2020 23:28:02: 13000000 INFO @ Mon, 29 Jun 2020 23:28:04: 18000000 INFO @ Mon, 29 Jun 2020 23:28:08: 14000000 INFO @ Mon, 29 Jun 2020 23:28:10: 19000000 INFO @ Mon, 29 Jun 2020 23:28:13: 15000000 INFO @ Mon, 29 Jun 2020 23:28:16: 20000000 INFO @ Mon, 29 Jun 2020 23:28:19: 16000000 INFO @ Mon, 29 Jun 2020 23:28:21: 21000000 INFO @ Mon, 29 Jun 2020 23:28:24: 17000000 INFO @ Mon, 29 Jun 2020 23:28:27: 22000000 INFO @ Mon, 29 Jun 2020 23:28:30: 18000000 INFO @ Mon, 29 Jun 2020 23:28:31: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:28:32: 23000000 INFO @ Mon, 29 Jun 2020 23:28:35: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:28:35: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:28:35: #1 total tags in treatment: 23468946 INFO @ Mon, 29 Jun 2020 23:28:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:28:35: #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 23:28:35: #1 tags after filtering in treatment: 23468946 INFO @ Mon, 29 Jun 2020 23:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:28:35: #1 finished! INFO @ Mon, 29 Jun 2020 23:28:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:28:35: 19000000 INFO @ Mon, 29 Jun 2020 23:28:37: #2 number of paired peaks: 183 WARNING @ Mon, 29 Jun 2020 23:28:37: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Mon, 29 Jun 2020 23:28:37: start model_add_line... INFO @ Mon, 29 Jun 2020 23:28:37: start X-correlation... INFO @ Mon, 29 Jun 2020 23:28:37: end of X-cor INFO @ Mon, 29 Jun 2020 23:28:37: #2 finished! INFO @ Mon, 29 Jun 2020 23:28:37: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 23:28:37: #2 alternative fragment length(s) may be 1,46,575 bps INFO @ Mon, 29 Jun 2020 23:28:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.10_model.r WARNING @ Mon, 29 Jun 2020 23:28:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:28:37: #2 You may need to consider one of the other alternative d(s): 1,46,575 WARNING @ Mon, 29 Jun 2020 23:28:37: #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 23:28:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:28:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:28:41: 20000000 INFO @ Mon, 29 Jun 2020 23:28:46: 21000000 INFO @ Mon, 29 Jun 2020 23:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.05_summits.bed INFO @ Mon, 29 Jun 2020 23:28:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:28:51: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:28:57: 23000000 INFO @ Mon, 29 Jun 2020 23:29:00: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:29:00: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:29:00: #1 total tags in treatment: 23468946 INFO @ Mon, 29 Jun 2020 23:29:00: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:29:00: #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 23:29:00: #1 tags after filtering in treatment: 23468946 INFO @ Mon, 29 Jun 2020 23:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:29:00: #1 finished! INFO @ Mon, 29 Jun 2020 23:29:00: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:29:01: #2 number of paired peaks: 183 WARNING @ Mon, 29 Jun 2020 23:29:01: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Mon, 29 Jun 2020 23:29:01: start model_add_line... INFO @ Mon, 29 Jun 2020 23:29:02: start X-correlation... INFO @ Mon, 29 Jun 2020 23:29:02: end of X-cor INFO @ Mon, 29 Jun 2020 23:29:02: #2 finished! INFO @ Mon, 29 Jun 2020 23:29:02: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 23:29:02: #2 alternative fragment length(s) may be 1,46,575 bps INFO @ Mon, 29 Jun 2020 23:29:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.20_model.r WARNING @ Mon, 29 Jun 2020 23:29:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:29:02: #2 You may need to consider one of the other alternative d(s): 1,46,575 WARNING @ Mon, 29 Jun 2020 23:29:02: #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 23:29:02: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:29:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:29:16: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.10_summits.bed INFO @ Mon, 29 Jun 2020 23:29:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:29:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:29:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:29:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3404020/SRX3404020.20_summits.bed INFO @ Mon, 29 Jun 2020 23:29:59: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling