Job ID = 6452679 SRX = SRX025481 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:45:45 prefetch.2.10.7: 1) Downloading 'SRR063884'... 2020-06-21T07:45:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:48:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:48:41 prefetch.2.10.7: 'SRR063884' is valid 2020-06-21T07:48:41 prefetch.2.10.7: 1) 'SRR063884' was downloaded successfully Read 18385800 spots for SRR063884/SRR063884.sra Written 18385800 spots for SRR063884/SRR063884.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: 00:03:42 18385800 reads; of these: 18385800 (100.00%) were unpaired; of these: 694321 (3.78%) aligned 0 times 14044802 (76.39%) aligned exactly 1 time 3646677 (19.83%) aligned >1 times 96.22% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 5415074 / 17691479 = 0.3061 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 16:56:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.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 16:56:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:56:15: 1000000 INFO @ Sun, 21 Jun 2020 16:56:20: 2000000 INFO @ Sun, 21 Jun 2020 16:56:25: 3000000 INFO @ Sun, 21 Jun 2020 16:56:30: 4000000 INFO @ Sun, 21 Jun 2020 16:56:35: 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 @ Sun, 21 Jun 2020 16:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.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 16:56:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:56:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:56:40: 6000000 INFO @ Sun, 21 Jun 2020 16:56:46: 7000000 INFO @ Sun, 21 Jun 2020 16:56:46: 1000000 INFO @ Sun, 21 Jun 2020 16:56:51: 8000000 INFO @ Sun, 21 Jun 2020 16:56:51: 2000000 INFO @ Sun, 21 Jun 2020 16:56:57: 9000000 INFO @ Sun, 21 Jun 2020 16:56:57: 3000000 INFO @ Sun, 21 Jun 2020 16:57:03: 10000000 INFO @ Sun, 21 Jun 2020 16:57:03: 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 @ Sun, 21 Jun 2020 16:57:09: 11000000 INFO @ Sun, 21 Jun 2020 16:57:09: 5000000 INFO @ Sun, 21 Jun 2020 16:57:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.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 16:57:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:14: 12000000 INFO @ Sun, 21 Jun 2020 16:57:15: 6000000 INFO @ Sun, 21 Jun 2020 16:57:16: 1000000 INFO @ Sun, 21 Jun 2020 16:57:16: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:57:16: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:57:16: #1 total tags in treatment: 12276405 INFO @ Sun, 21 Jun 2020 16:57:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:16: #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 16:57:17: #1 tags after filtering in treatment: 12276403 INFO @ Sun, 21 Jun 2020 16:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:17: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:57:17: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 16:57:17: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 16:57:17: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:17: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:17: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:17: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:17: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 16:57:17: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 16:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.05_model.r WARNING @ Sun, 21 Jun 2020 16:57:17: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:57:17: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 16:57:17: #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 16:57:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:57:20: 7000000 INFO @ Sun, 21 Jun 2020 16:57:22: 2000000 INFO @ Sun, 21 Jun 2020 16:57:26: 8000000 INFO @ Sun, 21 Jun 2020 16:57:27: 3000000 INFO @ Sun, 21 Jun 2020 16:57:31: 9000000 INFO @ Sun, 21 Jun 2020 16:57:33: 4000000 INFO @ Sun, 21 Jun 2020 16:57:37: 10000000 INFO @ Sun, 21 Jun 2020 16:57:39: 5000000 INFO @ Sun, 21 Jun 2020 16:57:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:57:43: 11000000 INFO @ Sun, 21 Jun 2020 16:57:45: 6000000 INFO @ Sun, 21 Jun 2020 16:57:49: 12000000 INFO @ Sun, 21 Jun 2020 16:57:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:57:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:57:50: #1 total tags in treatment: 12276405 INFO @ Sun, 21 Jun 2020 16:57:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:50: #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 16:57:51: 7000000 INFO @ Sun, 21 Jun 2020 16:57:51: #1 tags after filtering in treatment: 12276403 INFO @ Sun, 21 Jun 2020 16:57:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:51: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:57:52: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 16:57:52: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 16:57:52: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:52: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:52: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:52: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:52: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 16:57:52: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 16:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.10_model.r WARNING @ Sun, 21 Jun 2020 16:57:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:57:52: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 16:57:52: #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 16:57:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:57:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:57:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:57:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.05_summits.bed INFO @ Sun, 21 Jun 2020 16:57:53: Done! pass1 - making usageList (391 chroms): 1 millis pass2 - checking and writing primary data (1007 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:57:56: 8000000 INFO @ Sun, 21 Jun 2020 16:58:01: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:58:06: 10000000 INFO @ Sun, 21 Jun 2020 16:58:11: 11000000 INFO @ Sun, 21 Jun 2020 16:58:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:17: 12000000 INFO @ Sun, 21 Jun 2020 16:58:18: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:18: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:18: #1 total tags in treatment: 12276405 INFO @ Sun, 21 Jun 2020 16:58:18: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:18: #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 16:58:19: #1 tags after filtering in treatment: 12276403 INFO @ Sun, 21 Jun 2020 16:58:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:19: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:19: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 16:58:19: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 16:58:19: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:19: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:19: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:19: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:19: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 16:58:19: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 21 Jun 2020 16:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.20_model.r WARNING @ Sun, 21 Jun 2020 16:58:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:58:20: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 21 Jun 2020 16:58:20: #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 16:58:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.10_summits.bed INFO @ Sun, 21 Jun 2020 16:58:28: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (357 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:58:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025481/SRX025481.20_summits.bed INFO @ Sun, 21 Jun 2020 16:58:56: Done! pass1 - making usageList (85 chroms): 0 millis pass2 - checking and writing primary data (217 records, 4 fields): 4 millis CompletedMACS2peakCalling