Job ID = 6455003 SRX = SRX2618549 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:50:40 prefetch.2.10.7: 1) Downloading 'SRR5319103'... 2020-06-21T09:50:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:52:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:52:35 prefetch.2.10.7: 'SRR5319103' is valid 2020-06-21T09:52:35 prefetch.2.10.7: 1) 'SRR5319103' was downloaded successfully 2020-06-21T09:52:35 prefetch.2.10.7: 'SRR5319103' has 0 unresolved dependencies Read 18681022 spots for SRR5319103/SRR5319103.sra Written 18681022 spots for SRR5319103/SRR5319103.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: 00:05:20 18681022 reads; of these: 18681022 (100.00%) were unpaired; of these: 791754 (4.24%) aligned 0 times 11835841 (63.36%) aligned exactly 1 time 6053427 (32.40%) aligned >1 times 95.76% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 3146975 / 17889268 = 0.1759 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 19:02:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.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 19:02:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:05: 1000000 INFO @ Sun, 21 Jun 2020 19:03:11: 2000000 INFO @ Sun, 21 Jun 2020 19:03:17: 3000000 INFO @ Sun, 21 Jun 2020 19:03:24: 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 19:03:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.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 19:03:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:30: 5000000 INFO @ Sun, 21 Jun 2020 19:03:35: 1000000 INFO @ Sun, 21 Jun 2020 19:03:37: 6000000 INFO @ Sun, 21 Jun 2020 19:03:41: 2000000 INFO @ Sun, 21 Jun 2020 19:03:44: 7000000 INFO @ Sun, 21 Jun 2020 19:03:48: 3000000 INFO @ Sun, 21 Jun 2020 19:03:51: 8000000 INFO @ Sun, 21 Jun 2020 19:03:54: 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 19:03:57: 9000000 INFO @ Sun, 21 Jun 2020 19:03:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.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 19:03:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:01: 5000000 INFO @ Sun, 21 Jun 2020 19:04:04: 10000000 INFO @ Sun, 21 Jun 2020 19:04:05: 1000000 INFO @ Sun, 21 Jun 2020 19:04:07: 6000000 INFO @ Sun, 21 Jun 2020 19:04:10: 11000000 INFO @ Sun, 21 Jun 2020 19:04:11: 2000000 INFO @ Sun, 21 Jun 2020 19:04:14: 7000000 INFO @ Sun, 21 Jun 2020 19:04:17: 12000000 INFO @ Sun, 21 Jun 2020 19:04:18: 3000000 INFO @ Sun, 21 Jun 2020 19:04:21: 8000000 INFO @ Sun, 21 Jun 2020 19:04:24: 13000000 INFO @ Sun, 21 Jun 2020 19:04:25: 4000000 INFO @ Sun, 21 Jun 2020 19:04:27: 9000000 INFO @ Sun, 21 Jun 2020 19:04:31: 14000000 INFO @ Sun, 21 Jun 2020 19:04:31: 5000000 INFO @ Sun, 21 Jun 2020 19:04:34: 10000000 INFO @ Sun, 21 Jun 2020 19:04:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:36: #1 total tags in treatment: 14742293 INFO @ Sun, 21 Jun 2020 19:04:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:36: #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 19:04:36: #1 tags after filtering in treatment: 14742293 INFO @ Sun, 21 Jun 2020 19:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:37: #2 number of paired peaks: 843 WARNING @ Sun, 21 Jun 2020 19:04:37: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:37: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:04:37: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:04:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.05_model.r WARNING @ Sun, 21 Jun 2020 19:04:37: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:37: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:04:37: #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 19:04:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:38: 6000000 INFO @ Sun, 21 Jun 2020 19:04:40: 11000000 INFO @ Sun, 21 Jun 2020 19:04:45: 7000000 INFO @ Sun, 21 Jun 2020 19:04:47: 12000000 INFO @ Sun, 21 Jun 2020 19:04:51: 8000000 INFO @ Sun, 21 Jun 2020 19:04:54: 13000000 INFO @ Sun, 21 Jun 2020 19:04:58: 9000000 INFO @ Sun, 21 Jun 2020 19:05:00: 14000000 INFO @ Sun, 21 Jun 2020 19:05:04: 10000000 INFO @ Sun, 21 Jun 2020 19:05:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:05: #1 total tags in treatment: 14742293 INFO @ Sun, 21 Jun 2020 19:05:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:05:06: #1 tags after filtering in treatment: 14742293 INFO @ Sun, 21 Jun 2020 19:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:07: #2 number of paired peaks: 843 WARNING @ Sun, 21 Jun 2020 19:05:07: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:07: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:05:07: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.10_model.r WARNING @ Sun, 21 Jun 2020 19:05:07: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:05:07: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:05:07: #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 19:05:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:11: 11000000 INFO @ Sun, 21 Jun 2020 19:05:17: 12000000 INFO @ Sun, 21 Jun 2020 19:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.05_summits.bed INFO @ Sun, 21 Jun 2020 19:05:21: Done! pass1 - making usageList (663 chroms): 1 millis pass2 - checking and writing primary data (2525 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:24: 13000000 INFO @ Sun, 21 Jun 2020 19:05:30: 14000000 INFO @ Sun, 21 Jun 2020 19:05:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:35: #1 total tags in treatment: 14742293 INFO @ Sun, 21 Jun 2020 19:05:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:35: #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 19:05:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:35: #1 tags after filtering in treatment: 14742293 INFO @ Sun, 21 Jun 2020 19:05:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:36: #2 number of paired peaks: 843 WARNING @ Sun, 21 Jun 2020 19:05:36: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:36: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:05:36: #2 alternative fragment length(s) may be 3,36 bps INFO @ Sun, 21 Jun 2020 19:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.20_model.r WARNING @ Sun, 21 Jun 2020 19:05:36: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:05:36: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Sun, 21 Jun 2020 19:05:36: #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 19:05:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:50: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (2103 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:06:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618549/SRX2618549.20_summits.bed INFO @ Sun, 21 Jun 2020 19:06:20: Done! pass1 - making usageList (389 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 12 millis CompletedMACS2peakCalling