Job ID = 6454829 SRX = SRX2592425 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:43:40 prefetch.2.10.7: 1) Downloading 'SRR5289702'... 2020-06-21T09:43:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:46:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:46:13 prefetch.2.10.7: 1) 'SRR5289702' was downloaded successfully Read 17210489 spots for SRR5289702/SRR5289702.sra Written 17210489 spots for SRR5289702/SRR5289702.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: 00:05:48 17210489 reads; of these: 17210489 (100.00%) were unpaired; of these: 1280711 (7.44%) aligned 0 times 11814004 (68.64%) aligned exactly 1 time 4115774 (23.91%) aligned >1 times 92.56% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3614269 / 15929778 = 0.2269 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 @ Sun, 21 Jun 2020 18:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.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 @ Sun, 21 Jun 2020 18:57:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:26: 1000000 INFO @ Sun, 21 Jun 2020 18:57:32: 2000000 INFO @ Sun, 21 Jun 2020 18:57:38: 3000000 INFO @ Sun, 21 Jun 2020 18:57:44: 4000000 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 @ Sun, 21 Jun 2020 18:57:50: 5000000 INFO @ Sun, 21 Jun 2020 18:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.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 @ Sun, 21 Jun 2020 18:57:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:57: 6000000 INFO @ Sun, 21 Jun 2020 18:57:58: 1000000 INFO @ Sun, 21 Jun 2020 18:58:05: 7000000 INFO @ Sun, 21 Jun 2020 18:58:06: 2000000 INFO @ Sun, 21 Jun 2020 18:58:12: 8000000 INFO @ Sun, 21 Jun 2020 18:58:14: 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 @ Sun, 21 Jun 2020 18:58:20: 9000000 INFO @ Sun, 21 Jun 2020 18:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.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 @ Sun, 21 Jun 2020 18:58:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:22: 4000000 INFO @ Sun, 21 Jun 2020 18:58:28: 1000000 INFO @ Sun, 21 Jun 2020 18:58:28: 10000000 INFO @ Sun, 21 Jun 2020 18:58:30: 5000000 INFO @ Sun, 21 Jun 2020 18:58:35: 2000000 INFO @ Sun, 21 Jun 2020 18:58:35: 11000000 INFO @ Sun, 21 Jun 2020 18:58:38: 6000000 INFO @ Sun, 21 Jun 2020 18:58:43: 3000000 INFO @ Sun, 21 Jun 2020 18:58:43: 12000000 INFO @ Sun, 21 Jun 2020 18:58:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:58:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:58:46: #1 total tags in treatment: 12315509 INFO @ Sun, 21 Jun 2020 18:58:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:58:46: 7000000 INFO @ Sun, 21 Jun 2020 18:58:46: #1 tags after filtering in treatment: 12315398 INFO @ Sun, 21 Jun 2020 18:58:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:47: #2 number of paired peaks: 305 WARNING @ Sun, 21 Jun 2020 18:58:47: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 21 Jun 2020 18:58:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:47: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:58:47: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 21 Jun 2020 18:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.05_model.r WARNING @ Sun, 21 Jun 2020 18:58:47: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:47: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 21 Jun 2020 18:58:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:58:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:50: 4000000 INFO @ Sun, 21 Jun 2020 18:58:54: 8000000 INFO @ Sun, 21 Jun 2020 18:58:58: 5000000 INFO @ Sun, 21 Jun 2020 18:59:02: 9000000 INFO @ Sun, 21 Jun 2020 18:59:06: 6000000 INFO @ Sun, 21 Jun 2020 18:59:10: 10000000 INFO @ Sun, 21 Jun 2020 18:59:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:59:13: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:59:18: 11000000 INFO @ Sun, 21 Jun 2020 18:59:21: 8000000 INFO @ Sun, 21 Jun 2020 18:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.05_summits.bed INFO @ Sun, 21 Jun 2020 18:59:25: Done! pass1 - making usageList (684 chroms): 3 millis pass2 - checking and writing primary data (14005 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:59:27: 12000000 INFO @ Sun, 21 Jun 2020 18:59:28: 9000000 INFO @ Sun, 21 Jun 2020 18:59:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:59:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:59:29: #1 total tags in treatment: 12315509 INFO @ Sun, 21 Jun 2020 18:59:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:59:30: #1 tags after filtering in treatment: 12315398 INFO @ Sun, 21 Jun 2020 18:59:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:30: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:31: #2 number of paired peaks: 305 WARNING @ Sun, 21 Jun 2020 18:59:31: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 21 Jun 2020 18:59:31: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:31: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:31: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:31: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:31: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:59:31: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 21 Jun 2020 18:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.10_model.r WARNING @ Sun, 21 Jun 2020 18:59:31: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:59:31: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 21 Jun 2020 18:59:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:59:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:59:35: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:59:41: 11000000 INFO @ Sun, 21 Jun 2020 18:59:47: 12000000 INFO @ Sun, 21 Jun 2020 18:59:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:59:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:59:49: #1 total tags in treatment: 12315509 INFO @ Sun, 21 Jun 2020 18:59:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:59:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:59:50: #1 tags after filtering in treatment: 12315398 INFO @ Sun, 21 Jun 2020 18:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:59:50: #1 finished! INFO @ Sun, 21 Jun 2020 18:59:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:59:51: #2 number of paired peaks: 305 WARNING @ Sun, 21 Jun 2020 18:59:51: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Sun, 21 Jun 2020 18:59:51: start model_add_line... INFO @ Sun, 21 Jun 2020 18:59:51: start X-correlation... INFO @ Sun, 21 Jun 2020 18:59:51: end of X-cor INFO @ Sun, 21 Jun 2020 18:59:51: #2 finished! INFO @ Sun, 21 Jun 2020 18:59:51: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:59:51: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 21 Jun 2020 18:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.20_model.r WARNING @ Sun, 21 Jun 2020 18:59:51: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:59:51: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 21 Jun 2020 18:59:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:59:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:59:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.10_summits.bed INFO @ Sun, 21 Jun 2020 19:00:07: Done! pass1 - making usageList (459 chroms): 2 millis pass2 - checking and writing primary data (8770 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:00:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592425/SRX2592425.20_summits.bed INFO @ Sun, 21 Jun 2020 19:00:28: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (2222 records, 4 fields): 9 millis CompletedMACS2peakCalling