Job ID = 6456288 SRX = SRX335493 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:43:08 prefetch.2.10.7: 1) Downloading 'SRR952835'... 2020-06-21T10:43:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:49:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:49:20 prefetch.2.10.7: 1) 'SRR952835' was downloaded successfully Read 22570048 spots for SRR952835/SRR952835.sra Written 22570048 spots for SRR952835/SRR952835.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:30 22570048 reads; of these: 22570048 (100.00%) were unpaired; of these: 4624178 (20.49%) aligned 0 times 15704022 (69.58%) aligned exactly 1 time 2241848 (9.93%) aligned >1 times 79.51% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 3811753 / 17945870 = 0.2124 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 19:59:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.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 19:59:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:59:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:59:39: 1000000 INFO @ Sun, 21 Jun 2020 19:59:44: 2000000 INFO @ Sun, 21 Jun 2020 19:59:49: 3000000 INFO @ Sun, 21 Jun 2020 19:59:55: 4000000 INFO @ Sun, 21 Jun 2020 20:00:00: 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 20:00:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.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 20:00:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:00:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:00:05: 6000000 INFO @ Sun, 21 Jun 2020 20:00:09: 1000000 INFO @ Sun, 21 Jun 2020 20:00:11: 7000000 INFO @ Sun, 21 Jun 2020 20:00:15: 2000000 INFO @ Sun, 21 Jun 2020 20:00:17: 8000000 INFO @ Sun, 21 Jun 2020 20:00:20: 3000000 INFO @ Sun, 21 Jun 2020 20:00:22: 9000000 INFO @ Sun, 21 Jun 2020 20:00:26: 4000000 INFO @ Sun, 21 Jun 2020 20:00:28: 10000000 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 20:00:32: 5000000 INFO @ Sun, 21 Jun 2020 20:00:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.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 20:00:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:00:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:00:34: 11000000 INFO @ Sun, 21 Jun 2020 20:00:38: 6000000 INFO @ Sun, 21 Jun 2020 20:00:39: 1000000 INFO @ Sun, 21 Jun 2020 20:00:40: 12000000 INFO @ Sun, 21 Jun 2020 20:00:44: 7000000 INFO @ Sun, 21 Jun 2020 20:00:45: 2000000 INFO @ Sun, 21 Jun 2020 20:00:46: 13000000 INFO @ Sun, 21 Jun 2020 20:00:49: 8000000 INFO @ Sun, 21 Jun 2020 20:00:51: 3000000 INFO @ Sun, 21 Jun 2020 20:00:52: 14000000 INFO @ Sun, 21 Jun 2020 20:00:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:00:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:00:53: #1 total tags in treatment: 14134117 INFO @ Sun, 21 Jun 2020 20:00:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:00:53: #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 20:00:53: #1 tags after filtering in treatment: 14134093 INFO @ Sun, 21 Jun 2020 20:00:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:00:53: #1 finished! INFO @ Sun, 21 Jun 2020 20:00:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:00:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:00:54: #2 number of paired peaks: 135 WARNING @ Sun, 21 Jun 2020 20:00:54: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sun, 21 Jun 2020 20:00:54: start model_add_line... INFO @ Sun, 21 Jun 2020 20:00:55: start X-correlation... INFO @ Sun, 21 Jun 2020 20:00:55: end of X-cor INFO @ Sun, 21 Jun 2020 20:00:55: #2 finished! INFO @ Sun, 21 Jun 2020 20:00:55: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 20:00:55: #2 alternative fragment length(s) may be 4 bps INFO @ Sun, 21 Jun 2020 20:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.05_model.r WARNING @ Sun, 21 Jun 2020 20:00:55: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:00:55: #2 You may need to consider one of the other alternative d(s): 4 WARNING @ Sun, 21 Jun 2020 20:00:55: #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 20:00:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:00:55: 9000000 INFO @ Sun, 21 Jun 2020 20:00:57: 4000000 INFO @ Sun, 21 Jun 2020 20:01:01: 10000000 INFO @ Sun, 21 Jun 2020 20:01:03: 5000000 INFO @ Sun, 21 Jun 2020 20:01:07: 11000000 INFO @ Sun, 21 Jun 2020 20:01:09: 6000000 INFO @ Sun, 21 Jun 2020 20:01:13: 12000000 INFO @ Sun, 21 Jun 2020 20:01:15: 7000000 INFO @ Sun, 21 Jun 2020 20:01:19: 13000000 INFO @ Sun, 21 Jun 2020 20:01:21: 8000000 INFO @ Sun, 21 Jun 2020 20:01:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:25: 14000000 INFO @ Sun, 21 Jun 2020 20:01:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:01:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:01:26: #1 total tags in treatment: 14134117 INFO @ Sun, 21 Jun 2020 20:01:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:01:26: #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 20:01:26: #1 tags after filtering in treatment: 14134093 INFO @ Sun, 21 Jun 2020 20:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:01:26: #1 finished! INFO @ Sun, 21 Jun 2020 20:01:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:01:26: 9000000 INFO @ Sun, 21 Jun 2020 20:01:27: #2 number of paired peaks: 135 WARNING @ Sun, 21 Jun 2020 20:01:27: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sun, 21 Jun 2020 20:01:27: start model_add_line... INFO @ Sun, 21 Jun 2020 20:01:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:01:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:01:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:01:27: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 20:01:27: #2 alternative fragment length(s) may be 4 bps INFO @ Sun, 21 Jun 2020 20:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.10_model.r WARNING @ Sun, 21 Jun 2020 20:01:27: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:01:27: #2 You may need to consider one of the other alternative d(s): 4 WARNING @ Sun, 21 Jun 2020 20:01:27: #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 20:01:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:01:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:01:32: 10000000 INFO @ Sun, 21 Jun 2020 20:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.05_summits.bed INFO @ Sun, 21 Jun 2020 20:01:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:01:37: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:01:43: 12000000 INFO @ Sun, 21 Jun 2020 20:01:49: 13000000 INFO @ Sun, 21 Jun 2020 20:01:54: 14000000 INFO @ Sun, 21 Jun 2020 20:01:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:01:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:01:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:01:55: #1 total tags in treatment: 14134117 INFO @ Sun, 21 Jun 2020 20:01:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:01:55: #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 20:01:55: #1 tags after filtering in treatment: 14134093 INFO @ Sun, 21 Jun 2020 20:01:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:01:55: #1 finished! INFO @ Sun, 21 Jun 2020 20:01:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:01:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:01:56: #2 number of paired peaks: 135 WARNING @ Sun, 21 Jun 2020 20:01:56: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sun, 21 Jun 2020 20:01:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:01:56: start X-correlation... INFO @ Sun, 21 Jun 2020 20:01:56: end of X-cor INFO @ Sun, 21 Jun 2020 20:01:56: #2 finished! INFO @ Sun, 21 Jun 2020 20:01:56: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 20:01:56: #2 alternative fragment length(s) may be 4 bps INFO @ Sun, 21 Jun 2020 20:01:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.20_model.r WARNING @ Sun, 21 Jun 2020 20:01:56: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:01:56: #2 You may need to consider one of the other alternative d(s): 4 WARNING @ Sun, 21 Jun 2020 20:01:56: #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 20:01:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:01:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:02:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.10_summits.bed INFO @ Sun, 21 Jun 2020 20:02:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:02:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335493/SRX335493.20_summits.bed INFO @ Sun, 21 Jun 2020 20:02:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling