Job ID = 6454996 SRX = SRX2618544 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:38:40 prefetch.2.10.7: 1) Downloading 'SRR5319098'... 2020-06-21T09:38:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:39 prefetch.2.10.7: 'SRR5319098' is valid 2020-06-21T09:41:39 prefetch.2.10.7: 1) 'SRR5319098' was downloaded successfully 2020-06-21T09:41:39 prefetch.2.10.7: 'SRR5319098' has 0 unresolved dependencies Read 20448975 spots for SRR5319098/SRR5319098.sra Written 20448975 spots for SRR5319098/SRR5319098.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: 00:05:55 20448975 reads; of these: 20448975 (100.00%) were unpaired; of these: 2079112 (10.17%) aligned 0 times 12272837 (60.02%) aligned exactly 1 time 6097026 (29.82%) aligned >1 times 89.83% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 2697168 / 18369863 = 0.1468 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 18:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.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 18:54:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:23: 1000000 INFO @ Sun, 21 Jun 2020 18:54:30: 2000000 INFO @ Sun, 21 Jun 2020 18:54:37: 3000000 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 18:54:44: 4000000 INFO @ Sun, 21 Jun 2020 18:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.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 18:54:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:52: 5000000 INFO @ Sun, 21 Jun 2020 18:54:53: 1000000 INFO @ Sun, 21 Jun 2020 18:55:00: 6000000 INFO @ Sun, 21 Jun 2020 18:55:01: 2000000 INFO @ Sun, 21 Jun 2020 18:55:07: 7000000 INFO @ Sun, 21 Jun 2020 18:55:08: 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 18:55:15: 4000000 INFO @ Sun, 21 Jun 2020 18:55:15: 8000000 INFO @ Sun, 21 Jun 2020 18:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.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 18:55:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:22: 5000000 INFO @ Sun, 21 Jun 2020 18:55:23: 9000000 INFO @ Sun, 21 Jun 2020 18:55:24: 1000000 INFO @ Sun, 21 Jun 2020 18:55:30: 6000000 INFO @ Sun, 21 Jun 2020 18:55:30: 10000000 INFO @ Sun, 21 Jun 2020 18:55:31: 2000000 INFO @ Sun, 21 Jun 2020 18:55:37: 7000000 INFO @ Sun, 21 Jun 2020 18:55:38: 11000000 INFO @ Sun, 21 Jun 2020 18:55:38: 3000000 INFO @ Sun, 21 Jun 2020 18:55:44: 8000000 INFO @ Sun, 21 Jun 2020 18:55:46: 4000000 INFO @ Sun, 21 Jun 2020 18:55:46: 12000000 INFO @ Sun, 21 Jun 2020 18:55:51: 9000000 INFO @ Sun, 21 Jun 2020 18:55:53: 5000000 INFO @ Sun, 21 Jun 2020 18:55:54: 13000000 INFO @ Sun, 21 Jun 2020 18:55:58: 10000000 INFO @ Sun, 21 Jun 2020 18:56:00: 6000000 INFO @ Sun, 21 Jun 2020 18:56:02: 14000000 INFO @ Sun, 21 Jun 2020 18:56:06: 11000000 INFO @ Sun, 21 Jun 2020 18:56:07: 7000000 INFO @ Sun, 21 Jun 2020 18:56:10: 15000000 INFO @ Sun, 21 Jun 2020 18:56:13: 12000000 INFO @ Sun, 21 Jun 2020 18:56:14: 8000000 INFO @ Sun, 21 Jun 2020 18:56:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:56:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:56:15: #1 total tags in treatment: 15672695 INFO @ Sun, 21 Jun 2020 18:56:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:15: #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 18:56:15: #1 tags after filtering in treatment: 15672695 INFO @ Sun, 21 Jun 2020 18:56:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:17: #2 number of paired peaks: 913 WARNING @ Sun, 21 Jun 2020 18:56:17: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Sun, 21 Jun 2020 18:56:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:17: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:56:17: #2 alternative fragment length(s) may be 2,21 bps INFO @ Sun, 21 Jun 2020 18:56:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.05_model.r WARNING @ Sun, 21 Jun 2020 18:56:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:56:17: #2 You may need to consider one of the other alternative d(s): 2,21 WARNING @ Sun, 21 Jun 2020 18:56:17: #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 18:56:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:20: 13000000 INFO @ Sun, 21 Jun 2020 18:56:21: 9000000 INFO @ Sun, 21 Jun 2020 18:56:26: 14000000 INFO @ Sun, 21 Jun 2020 18:56:27: 10000000 INFO @ Sun, 21 Jun 2020 18:56:33: 15000000 INFO @ Sun, 21 Jun 2020 18:56:34: 11000000 INFO @ Sun, 21 Jun 2020 18:56:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:56:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:56:37: #1 total tags in treatment: 15672695 INFO @ Sun, 21 Jun 2020 18:56:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:37: #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 18:56:38: #1 tags after filtering in treatment: 15672695 INFO @ Sun, 21 Jun 2020 18:56:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:39: #2 number of paired peaks: 913 WARNING @ Sun, 21 Jun 2020 18:56:39: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Sun, 21 Jun 2020 18:56:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:39: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:56:39: #2 alternative fragment length(s) may be 2,21 bps INFO @ Sun, 21 Jun 2020 18:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.10_model.r WARNING @ Sun, 21 Jun 2020 18:56:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:56:39: #2 You may need to consider one of the other alternative d(s): 2,21 WARNING @ Sun, 21 Jun 2020 18:56:39: #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 18:56:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:40: 12000000 INFO @ Sun, 21 Jun 2020 18:56:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:56:46: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:56:52: 14000000 INFO @ Sun, 21 Jun 2020 18:56:58: 15000000 INFO @ Sun, 21 Jun 2020 18:56:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:56:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:56:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.05_summits.bed INFO @ Sun, 21 Jun 2020 18:56:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:57:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:57:02: #1 total tags in treatment: 15672695 INFO @ Sun, 21 Jun 2020 18:57:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:02: #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 18:57:02: #1 tags after filtering in treatment: 15672695 INFO @ Sun, 21 Jun 2020 18:57:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:03: #2 number of paired peaks: 913 WARNING @ Sun, 21 Jun 2020 18:57:03: Fewer paired peaks (913) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 913 pairs to build model! INFO @ Sun, 21 Jun 2020 18:57:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:03: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 18:57:03: #2 alternative fragment length(s) may be 2,21 bps INFO @ Sun, 21 Jun 2020 18:57:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.20_model.r WARNING @ Sun, 21 Jun 2020 18:57:03: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:57:03: #2 You may need to consider one of the other alternative d(s): 2,21 WARNING @ Sun, 21 Jun 2020 18:57:03: #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 18:57:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.10_summits.bed INFO @ Sun, 21 Jun 2020 18:57:21: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618544/SRX2618544.20_summits.bed INFO @ Sun, 21 Jun 2020 18:57:46: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling