Job ID = 6528101 SRX = SRX4664658 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:11:50 prefetch.2.10.7: 1) Downloading 'SRR7813085'... 2020-06-29T14:11:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:14:00 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:14:00 prefetch.2.10.7: 1) 'SRR7813085' was downloaded successfully Read 29764677 spots for SRR7813085/SRR7813085.sra Written 29764677 spots for SRR7813085/SRR7813085.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: 00:10:17 29764677 reads; of these: 29764677 (100.00%) were unpaired; of these: 705215 (2.37%) aligned 0 times 20775515 (69.80%) aligned exactly 1 time 8283947 (27.83%) aligned >1 times 97.63% overall alignment rate Time searching: 00:10:17 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] 3407377 / 29059462 = 0.1173 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 23:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.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 23:41:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:41:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:41:51: 1000000 INFO @ Mon, 29 Jun 2020 23:41:57: 2000000 INFO @ Mon, 29 Jun 2020 23:42:02: 3000000 INFO @ Mon, 29 Jun 2020 23:42:08: 4000000 INFO @ Mon, 29 Jun 2020 23:42:13: 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 23:42:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.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 23:42:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:42:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:42:18: 6000000 INFO @ Mon, 29 Jun 2020 23:42:22: 1000000 INFO @ Mon, 29 Jun 2020 23:42:23: 7000000 INFO @ Mon, 29 Jun 2020 23:42:28: 2000000 INFO @ Mon, 29 Jun 2020 23:42:29: 8000000 INFO @ Mon, 29 Jun 2020 23:42:34: 9000000 INFO @ Mon, 29 Jun 2020 23:42:34: 3000000 INFO @ Mon, 29 Jun 2020 23:42:39: 10000000 INFO @ Mon, 29 Jun 2020 23:42:40: 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 23:42:44: 11000000 INFO @ Mon, 29 Jun 2020 23:42:45: 5000000 INFO @ Mon, 29 Jun 2020 23:42:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.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 23:42:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:42:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:42:50: 12000000 INFO @ Mon, 29 Jun 2020 23:42:50: 6000000 INFO @ Mon, 29 Jun 2020 23:42:52: 1000000 INFO @ Mon, 29 Jun 2020 23:42:55: 13000000 INFO @ Mon, 29 Jun 2020 23:42:56: 7000000 INFO @ Mon, 29 Jun 2020 23:42:57: 2000000 INFO @ Mon, 29 Jun 2020 23:43:00: 14000000 INFO @ Mon, 29 Jun 2020 23:43:01: 8000000 INFO @ Mon, 29 Jun 2020 23:43:03: 3000000 INFO @ Mon, 29 Jun 2020 23:43:06: 15000000 INFO @ Mon, 29 Jun 2020 23:43:07: 9000000 INFO @ Mon, 29 Jun 2020 23:43:08: 4000000 INFO @ Mon, 29 Jun 2020 23:43:12: 16000000 INFO @ Mon, 29 Jun 2020 23:43:12: 10000000 INFO @ Mon, 29 Jun 2020 23:43:14: 5000000 INFO @ Mon, 29 Jun 2020 23:43:17: 17000000 INFO @ Mon, 29 Jun 2020 23:43:18: 11000000 INFO @ Mon, 29 Jun 2020 23:43:19: 6000000 INFO @ Mon, 29 Jun 2020 23:43:23: 18000000 INFO @ Mon, 29 Jun 2020 23:43:23: 12000000 INFO @ Mon, 29 Jun 2020 23:43:25: 7000000 INFO @ Mon, 29 Jun 2020 23:43:28: 19000000 INFO @ Mon, 29 Jun 2020 23:43:29: 13000000 INFO @ Mon, 29 Jun 2020 23:43:30: 8000000 INFO @ Mon, 29 Jun 2020 23:43:34: 20000000 INFO @ Mon, 29 Jun 2020 23:43:35: 14000000 INFO @ Mon, 29 Jun 2020 23:43:36: 9000000 INFO @ Mon, 29 Jun 2020 23:43:40: 21000000 INFO @ Mon, 29 Jun 2020 23:43:40: 15000000 INFO @ Mon, 29 Jun 2020 23:43:41: 10000000 INFO @ Mon, 29 Jun 2020 23:43:45: 22000000 INFO @ Mon, 29 Jun 2020 23:43:46: 16000000 INFO @ Mon, 29 Jun 2020 23:43:47: 11000000 INFO @ Mon, 29 Jun 2020 23:43:51: 23000000 INFO @ Mon, 29 Jun 2020 23:43:52: 17000000 INFO @ Mon, 29 Jun 2020 23:43:53: 12000000 INFO @ Mon, 29 Jun 2020 23:43:57: 24000000 INFO @ Mon, 29 Jun 2020 23:43:58: 18000000 INFO @ Mon, 29 Jun 2020 23:43:59: 13000000 INFO @ Mon, 29 Jun 2020 23:44:03: 25000000 INFO @ Mon, 29 Jun 2020 23:44:04: 19000000 INFO @ Mon, 29 Jun 2020 23:44:05: 14000000 INFO @ Mon, 29 Jun 2020 23:44:07: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:44:07: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:44:07: #1 total tags in treatment: 25652085 INFO @ Mon, 29 Jun 2020 23:44:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:44:07: #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 23:44:08: #1 tags after filtering in treatment: 25652085 INFO @ Mon, 29 Jun 2020 23:44:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:44:08: #1 finished! INFO @ Mon, 29 Jun 2020 23:44:08: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:44:10: #2 number of paired peaks: 407 WARNING @ Mon, 29 Jun 2020 23:44:10: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Mon, 29 Jun 2020 23:44:10: start model_add_line... INFO @ Mon, 29 Jun 2020 23:44:10: 20000000 INFO @ Mon, 29 Jun 2020 23:44:10: start X-correlation... INFO @ Mon, 29 Jun 2020 23:44:10: end of X-cor INFO @ Mon, 29 Jun 2020 23:44:10: #2 finished! INFO @ Mon, 29 Jun 2020 23:44:10: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:44:10: #2 alternative fragment length(s) may be 2,21,565 bps INFO @ Mon, 29 Jun 2020 23:44:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.05_model.r WARNING @ Mon, 29 Jun 2020 23:44:10: #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 23:44:10: #2 You may need to consider one of the other alternative d(s): 2,21,565 WARNING @ Mon, 29 Jun 2020 23:44:10: #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 23:44:10: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:44:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:44:11: 15000000 INFO @ Mon, 29 Jun 2020 23:44:16: 21000000 INFO @ Mon, 29 Jun 2020 23:44:17: 16000000 INFO @ Mon, 29 Jun 2020 23:44:22: 22000000 INFO @ Mon, 29 Jun 2020 23:44:23: 17000000 INFO @ Mon, 29 Jun 2020 23:44:28: 23000000 INFO @ Mon, 29 Jun 2020 23:44:30: 18000000 INFO @ Mon, 29 Jun 2020 23:44:34: 24000000 INFO @ Mon, 29 Jun 2020 23:44:36: 19000000 INFO @ Mon, 29 Jun 2020 23:44:40: 25000000 INFO @ Mon, 29 Jun 2020 23:44:42: 20000000 INFO @ Mon, 29 Jun 2020 23:44:44: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:44:44: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:44:44: #1 total tags in treatment: 25652085 INFO @ Mon, 29 Jun 2020 23:44:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:44:44: #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 23:44:45: #1 tags after filtering in treatment: 25652085 INFO @ Mon, 29 Jun 2020 23:44:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:44:45: #1 finished! INFO @ Mon, 29 Jun 2020 23:44:45: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:44:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:44:46: #2 number of paired peaks: 407 WARNING @ Mon, 29 Jun 2020 23:44:46: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Mon, 29 Jun 2020 23:44:46: start model_add_line... INFO @ Mon, 29 Jun 2020 23:44:47: start X-correlation... INFO @ Mon, 29 Jun 2020 23:44:47: end of X-cor INFO @ Mon, 29 Jun 2020 23:44:47: #2 finished! INFO @ Mon, 29 Jun 2020 23:44:47: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:44:47: #2 alternative fragment length(s) may be 2,21,565 bps INFO @ Mon, 29 Jun 2020 23:44:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.10_model.r WARNING @ Mon, 29 Jun 2020 23:44:47: #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 23:44:47: #2 You may need to consider one of the other alternative d(s): 2,21,565 WARNING @ Mon, 29 Jun 2020 23:44:47: #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 23:44:47: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:44:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:44:48: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:44:48: 21000000 INFO @ Mon, 29 Jun 2020 23:44:54: 22000000 INFO @ Mon, 29 Jun 2020 23:45:00: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:45:06: 24000000 INFO @ Mon, 29 Jun 2020 23:45:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.05_summits.bed INFO @ Mon, 29 Jun 2020 23:45:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:45:12: 25000000 INFO @ Mon, 29 Jun 2020 23:45:16: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:45:16: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:45:16: #1 total tags in treatment: 25652085 INFO @ Mon, 29 Jun 2020 23:45:16: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:45:16: #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 23:45:16: #1 tags after filtering in treatment: 25652085 INFO @ Mon, 29 Jun 2020 23:45:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:45:16: #1 finished! INFO @ Mon, 29 Jun 2020 23:45:16: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:45:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:45:18: #2 number of paired peaks: 407 WARNING @ Mon, 29 Jun 2020 23:45:18: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Mon, 29 Jun 2020 23:45:18: start model_add_line... INFO @ Mon, 29 Jun 2020 23:45:18: start X-correlation... INFO @ Mon, 29 Jun 2020 23:45:18: end of X-cor INFO @ Mon, 29 Jun 2020 23:45:18: #2 finished! INFO @ Mon, 29 Jun 2020 23:45:18: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:45:18: #2 alternative fragment length(s) may be 2,21,565 bps INFO @ Mon, 29 Jun 2020 23:45:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.20_model.r WARNING @ Mon, 29 Jun 2020 23:45:18: #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 23:45:18: #2 You may need to consider one of the other alternative d(s): 2,21,565 WARNING @ Mon, 29 Jun 2020 23:45:18: #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 23:45:18: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:45:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:45:24: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.10_summits.bed INFO @ Mon, 29 Jun 2020 23:45:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:45:56: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:46:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:46:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:46:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664658/SRX4664658.20_summits.bed INFO @ Mon, 29 Jun 2020 23:46:15: 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。