Job ID = 6454137 SRX = SRX183883 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:51:19 prefetch.2.10.7: 1) Downloading 'SRR557678'... 2020-06-21T08:51:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:02:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:02:20 prefetch.2.10.7: 1) 'SRR557678' was downloaded successfully Read 32492092 spots for SRR557678/SRR557678.sra Written 32492092 spots for SRR557678/SRR557678.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: 00:06:54 32492092 reads; of these: 32492092 (100.00%) were unpaired; of these: 2262562 (6.96%) aligned 0 times 24533970 (75.51%) aligned exactly 1 time 5695560 (17.53%) aligned >1 times 93.04% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 17342614 / 30229530 = 0.5737 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 18:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.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 18:18:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:04: 1000000 INFO @ Sun, 21 Jun 2020 18:19:10: 2000000 INFO @ Sun, 21 Jun 2020 18:19:16: 3000000 INFO @ Sun, 21 Jun 2020 18:19:22: 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 18:19:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.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 18:19:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:29: 5000000 INFO @ Sun, 21 Jun 2020 18:19:34: 1000000 INFO @ Sun, 21 Jun 2020 18:19:35: 6000000 INFO @ Sun, 21 Jun 2020 18:19:40: 2000000 INFO @ Sun, 21 Jun 2020 18:19:41: 7000000 INFO @ Sun, 21 Jun 2020 18:19:47: 3000000 INFO @ Sun, 21 Jun 2020 18:19:48: 8000000 INFO @ Sun, 21 Jun 2020 18:19:53: 4000000 INFO @ Sun, 21 Jun 2020 18:19:54: 9000000 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 18:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.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 18:19:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:20:00: 5000000 INFO @ Sun, 21 Jun 2020 18:20:00: 10000000 INFO @ Sun, 21 Jun 2020 18:20:04: 1000000 INFO @ Sun, 21 Jun 2020 18:20:07: 6000000 INFO @ Sun, 21 Jun 2020 18:20:08: 11000000 INFO @ Sun, 21 Jun 2020 18:20:11: 2000000 INFO @ Sun, 21 Jun 2020 18:20:13: 7000000 INFO @ Sun, 21 Jun 2020 18:20:15: 12000000 INFO @ Sun, 21 Jun 2020 18:20:18: 3000000 INFO @ Sun, 21 Jun 2020 18:20:20: 8000000 INFO @ Sun, 21 Jun 2020 18:20:21: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:20:21: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:20:21: #1 total tags in treatment: 12886916 INFO @ Sun, 21 Jun 2020 18:20:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:21: #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 18:20:22: #1 tags after filtering in treatment: 12886878 INFO @ Sun, 21 Jun 2020 18:20:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:23: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 18:20:23: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:23: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 18:20:23: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 18:20:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:23: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:23: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sun, 21 Jun 2020 18:20:23: #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 18:20:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:24: 4000000 INFO @ Sun, 21 Jun 2020 18:20:27: 9000000 INFO @ Sun, 21 Jun 2020 18:20:30: 5000000 INFO @ Sun, 21 Jun 2020 18:20:33: 10000000 INFO @ Sun, 21 Jun 2020 18:20:37: 6000000 INFO @ Sun, 21 Jun 2020 18:20:40: 11000000 INFO @ Sun, 21 Jun 2020 18:20:43: 7000000 INFO @ Sun, 21 Jun 2020 18:20:47: 12000000 INFO @ Sun, 21 Jun 2020 18:20:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:50: 8000000 INFO @ Sun, 21 Jun 2020 18:20:53: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:20:53: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:20:53: #1 total tags in treatment: 12886916 INFO @ Sun, 21 Jun 2020 18:20:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:53: #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 18:20:54: #1 tags after filtering in treatment: 12886878 INFO @ Sun, 21 Jun 2020 18:20:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:55: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 18:20:55: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 18:20:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:55: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 18:20:55: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 18:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:55: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:55: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sun, 21 Jun 2020 18:20:55: #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 18:20:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:56: 9000000 INFO @ Sun, 21 Jun 2020 18:21:02: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.05_summits.bed INFO @ Sun, 21 Jun 2020 18:21:03: Done! pass1 - making usageList (858 chroms): 4 millis pass2 - checking and writing primary data (16534 records, 4 fields): 65 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:09: 11000000 INFO @ Sun, 21 Jun 2020 18:21:15: 12000000 INFO @ Sun, 21 Jun 2020 18:21:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:21: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 18:21:21: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 18:21:21: #1 total tags in treatment: 12886916 INFO @ Sun, 21 Jun 2020 18:21:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:21: #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 18:21:21: #1 tags after filtering in treatment: 12886878 INFO @ Sun, 21 Jun 2020 18:21:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:22: #2 number of paired peaks: 699 WARNING @ Sun, 21 Jun 2020 18:21:22: Fewer paired peaks (699) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 699 pairs to build model! INFO @ Sun, 21 Jun 2020 18:21:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:23: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 18:21:23: #2 alternative fragment length(s) may be 64 bps INFO @ Sun, 21 Jun 2020 18:21:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:23: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:23: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Sun, 21 Jun 2020 18:21:23: #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 18:21:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:34: Done! pass1 - making usageList (542 chroms): 2 millis pass2 - checking and writing primary data (6627 records, 4 fields): 36 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:22:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:22:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:22:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183883/SRX183883.20_summits.bed INFO @ Sun, 21 Jun 2020 18:22:02: Done! pass1 - making usageList (233 chroms): 2 millis pass2 - checking and writing primary data (2060 records, 4 fields): 16 millis CompletedMACS2peakCalling