Job ID = 6527772 SRX = SRX2831140 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:54:49 prefetch.2.10.7: 1) Downloading 'SRR5572462'... 2020-06-29T13:54:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:56:52 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:56:52 prefetch.2.10.7: 1) 'SRR5572462' was downloaded successfully Read 28625208 spots for SRR5572462/SRR5572462.sra Written 28625208 spots for SRR5572462/SRR5572462.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: 00:10:16 28625208 reads; of these: 28625208 (100.00%) were unpaired; of these: 1836587 (6.42%) aligned 0 times 20127031 (70.31%) aligned exactly 1 time 6661590 (23.27%) aligned >1 times 93.58% overall alignment rate Time searching: 00:10:16 Overall time: 00:10:17 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] 3292481 / 26788621 = 0.1229 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 23:24:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.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 23:24:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:24:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:24:17: 1000000 INFO @ Mon, 29 Jun 2020 23:24:25: 2000000 INFO @ Mon, 29 Jun 2020 23:24:32: 3000000 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 23:24:39: 4000000 INFO @ Mon, 29 Jun 2020 23:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.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 23:24:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:24:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:24:47: 5000000 INFO @ Mon, 29 Jun 2020 23:24:48: 1000000 INFO @ Mon, 29 Jun 2020 23:24:55: 6000000 INFO @ Mon, 29 Jun 2020 23:24:56: 2000000 INFO @ Mon, 29 Jun 2020 23:25:03: 7000000 INFO @ Mon, 29 Jun 2020 23:25:04: 3000000 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 23:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.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 23:25:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:25:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:25:11: 8000000 INFO @ Mon, 29 Jun 2020 23:25:12: 4000000 INFO @ Mon, 29 Jun 2020 23:25:17: 1000000 INFO @ Mon, 29 Jun 2020 23:25:20: 9000000 INFO @ Mon, 29 Jun 2020 23:25:21: 5000000 INFO @ Mon, 29 Jun 2020 23:25:23: 2000000 INFO @ Mon, 29 Jun 2020 23:25:28: 10000000 INFO @ Mon, 29 Jun 2020 23:25:29: 6000000 INFO @ Mon, 29 Jun 2020 23:25:30: 3000000 INFO @ Mon, 29 Jun 2020 23:25:36: 11000000 INFO @ Mon, 29 Jun 2020 23:25:37: 7000000 INFO @ Mon, 29 Jun 2020 23:25:37: 4000000 INFO @ Mon, 29 Jun 2020 23:25:44: 12000000 INFO @ Mon, 29 Jun 2020 23:25:44: 5000000 INFO @ Mon, 29 Jun 2020 23:25:45: 8000000 INFO @ Mon, 29 Jun 2020 23:25:51: 6000000 INFO @ Mon, 29 Jun 2020 23:25:52: 13000000 INFO @ Mon, 29 Jun 2020 23:25:53: 9000000 INFO @ Mon, 29 Jun 2020 23:25:58: 7000000 INFO @ Mon, 29 Jun 2020 23:26:00: 14000000 INFO @ Mon, 29 Jun 2020 23:26:01: 10000000 INFO @ Mon, 29 Jun 2020 23:26:05: 8000000 INFO @ Mon, 29 Jun 2020 23:26:08: 15000000 INFO @ Mon, 29 Jun 2020 23:26:09: 11000000 INFO @ Mon, 29 Jun 2020 23:26:12: 9000000 INFO @ Mon, 29 Jun 2020 23:26:16: 16000000 INFO @ Mon, 29 Jun 2020 23:26:17: 12000000 INFO @ Mon, 29 Jun 2020 23:26:19: 10000000 INFO @ Mon, 29 Jun 2020 23:26:24: 17000000 INFO @ Mon, 29 Jun 2020 23:26:25: 13000000 INFO @ Mon, 29 Jun 2020 23:26:26: 11000000 INFO @ Mon, 29 Jun 2020 23:26:32: 18000000 INFO @ Mon, 29 Jun 2020 23:26:33: 12000000 INFO @ Mon, 29 Jun 2020 23:26:33: 14000000 INFO @ Mon, 29 Jun 2020 23:26:39: 13000000 INFO @ Mon, 29 Jun 2020 23:26:40: 19000000 INFO @ Mon, 29 Jun 2020 23:26:41: 15000000 INFO @ Mon, 29 Jun 2020 23:26:46: 14000000 INFO @ Mon, 29 Jun 2020 23:26:48: 20000000 INFO @ Mon, 29 Jun 2020 23:26:49: 16000000 INFO @ Mon, 29 Jun 2020 23:26:53: 15000000 INFO @ Mon, 29 Jun 2020 23:26:56: 21000000 INFO @ Mon, 29 Jun 2020 23:26:57: 17000000 INFO @ Mon, 29 Jun 2020 23:27:00: 16000000 INFO @ Mon, 29 Jun 2020 23:27:04: 22000000 INFO @ Mon, 29 Jun 2020 23:27:06: 18000000 INFO @ Mon, 29 Jun 2020 23:27:07: 17000000 INFO @ Mon, 29 Jun 2020 23:27:12: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:27:14: 19000000 INFO @ Mon, 29 Jun 2020 23:27:14: 18000000 INFO @ Mon, 29 Jun 2020 23:27:16: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:27:16: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:27:16: #1 total tags in treatment: 23496140 INFO @ Mon, 29 Jun 2020 23:27:16: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:27:16: #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 23:27:16: #1 tags after filtering in treatment: 23496140 INFO @ Mon, 29 Jun 2020 23:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:27:16: #1 finished! INFO @ Mon, 29 Jun 2020 23:27:16: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:27:18: #2 number of paired peaks: 363 WARNING @ Mon, 29 Jun 2020 23:27:18: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Mon, 29 Jun 2020 23:27:18: start model_add_line... INFO @ Mon, 29 Jun 2020 23:27:18: start X-correlation... INFO @ Mon, 29 Jun 2020 23:27:18: end of X-cor INFO @ Mon, 29 Jun 2020 23:27:18: #2 finished! INFO @ Mon, 29 Jun 2020 23:27:18: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:27:18: #2 alternative fragment length(s) may be 2,24,593 bps INFO @ Mon, 29 Jun 2020 23:27:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.05_model.r WARNING @ Mon, 29 Jun 2020 23:27:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:27:18: #2 You may need to consider one of the other alternative d(s): 2,24,593 WARNING @ Mon, 29 Jun 2020 23:27:18: #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 23:27:18: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:27:21: 19000000 INFO @ Mon, 29 Jun 2020 23:27:21: 20000000 INFO @ Mon, 29 Jun 2020 23:27:28: 20000000 INFO @ Mon, 29 Jun 2020 23:27:29: 21000000 INFO @ Mon, 29 Jun 2020 23:27:34: 21000000 INFO @ Mon, 29 Jun 2020 23:27:37: 22000000 INFO @ Mon, 29 Jun 2020 23:27:41: 22000000 INFO @ Mon, 29 Jun 2020 23:27:44: 23000000 INFO @ Mon, 29 Jun 2020 23:27:48: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:27:48: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:27:48: #1 total tags in treatment: 23496140 INFO @ Mon, 29 Jun 2020 23:27:48: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:27:48: #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 23:27:48: 23000000 INFO @ Mon, 29 Jun 2020 23:27:48: #1 tags after filtering in treatment: 23496140 INFO @ Mon, 29 Jun 2020 23:27:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:27:48: #1 finished! INFO @ Mon, 29 Jun 2020 23:27:48: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:27:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:27:50: #2 number of paired peaks: 363 WARNING @ Mon, 29 Jun 2020 23:27:50: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Mon, 29 Jun 2020 23:27:50: start model_add_line... INFO @ Mon, 29 Jun 2020 23:27:50: start X-correlation... INFO @ Mon, 29 Jun 2020 23:27:50: end of X-cor INFO @ Mon, 29 Jun 2020 23:27:50: #2 finished! INFO @ Mon, 29 Jun 2020 23:27:50: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:27:50: #2 alternative fragment length(s) may be 2,24,593 bps INFO @ Mon, 29 Jun 2020 23:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.10_model.r WARNING @ Mon, 29 Jun 2020 23:27:50: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:27:50: #2 You may need to consider one of the other alternative d(s): 2,24,593 WARNING @ Mon, 29 Jun 2020 23:27:50: #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 23:27:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:27:52: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:27:52: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:27:52: #1 total tags in treatment: 23496140 INFO @ Mon, 29 Jun 2020 23:27:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:27:52: #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 23:27:52: #1 tags after filtering in treatment: 23496140 INFO @ Mon, 29 Jun 2020 23:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:27:52: #1 finished! INFO @ Mon, 29 Jun 2020 23:27:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:27:54: #2 number of paired peaks: 363 WARNING @ Mon, 29 Jun 2020 23:27:54: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Mon, 29 Jun 2020 23:27:54: start model_add_line... INFO @ Mon, 29 Jun 2020 23:27:54: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:27:54: start X-correlation... INFO @ Mon, 29 Jun 2020 23:27:54: end of X-cor INFO @ Mon, 29 Jun 2020 23:27:54: #2 finished! INFO @ Mon, 29 Jun 2020 23:27:54: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:27:54: #2 alternative fragment length(s) may be 2,24,593 bps INFO @ Mon, 29 Jun 2020 23:27:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.20_model.r WARNING @ Mon, 29 Jun 2020 23:27:54: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:27:54: #2 You may need to consider one of the other alternative d(s): 2,24,593 WARNING @ Mon, 29 Jun 2020 23:27:54: #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 23:27:54: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:27:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.05_summits.bed INFO @ Mon, 29 Jun 2020 23:28:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:28:26: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:28:29: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:28:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:28:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.10_summits.bed INFO @ Mon, 29 Jun 2020 23:28:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2831140/SRX2831140.20_summits.bed INFO @ Mon, 29 Jun 2020 23:28:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling