Job ID = 6527950 SRX = SRX335516 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:02:21 prefetch.2.10.7: 1) Downloading 'SRR952858'... 2020-06-29T14:02:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:04:55 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:04:55 prefetch.2.10.7: 1) 'SRR952858' was downloaded successfully Read 20447466 spots for SRR952858/SRR952858.sra Written 20447466 spots for SRR952858/SRR952858.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: 00:05:44 20447466 reads; of these: 20447466 (100.00%) were unpaired; of these: 2803932 (13.71%) aligned 0 times 12599991 (61.62%) aligned exactly 1 time 5043543 (24.67%) aligned >1 times 86.29% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3942782 / 17643534 = 0.2235 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 @ Mon, 29 Jun 2020 23:20:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.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 @ Mon, 29 Jun 2020 23:20:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:20:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:20:17: 1000000 INFO @ Mon, 29 Jun 2020 23:20:24: 2000000 INFO @ Mon, 29 Jun 2020 23:20:30: 3000000 INFO @ Mon, 29 Jun 2020 23:20:37: 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 @ Mon, 29 Jun 2020 23:20:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.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 @ Mon, 29 Jun 2020 23:20:41: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:20:41: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:20:43: 5000000 INFO @ Mon, 29 Jun 2020 23:20:48: 1000000 INFO @ Mon, 29 Jun 2020 23:20:50: 6000000 INFO @ Mon, 29 Jun 2020 23:20:54: 2000000 INFO @ Mon, 29 Jun 2020 23:20:58: 7000000 INFO @ Mon, 29 Jun 2020 23:21:01: 3000000 INFO @ Mon, 29 Jun 2020 23:21:05: 8000000 INFO @ Mon, 29 Jun 2020 23:21:07: 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 @ Mon, 29 Jun 2020 23:21:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.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 @ Mon, 29 Jun 2020 23:21:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:21:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:21:12: 9000000 INFO @ Mon, 29 Jun 2020 23:21:14: 5000000 INFO @ Mon, 29 Jun 2020 23:21:18: 1000000 INFO @ Mon, 29 Jun 2020 23:21:19: 10000000 INFO @ Mon, 29 Jun 2020 23:21:20: 6000000 INFO @ Mon, 29 Jun 2020 23:21:24: 2000000 INFO @ Mon, 29 Jun 2020 23:21:26: 11000000 INFO @ Mon, 29 Jun 2020 23:21:27: 7000000 INFO @ Mon, 29 Jun 2020 23:21:31: 3000000 INFO @ Mon, 29 Jun 2020 23:21:33: 12000000 INFO @ Mon, 29 Jun 2020 23:21:34: 8000000 INFO @ Mon, 29 Jun 2020 23:21:37: 4000000 INFO @ Mon, 29 Jun 2020 23:21:40: 9000000 INFO @ Mon, 29 Jun 2020 23:21:41: 13000000 INFO @ Mon, 29 Jun 2020 23:21:44: 5000000 INFO @ Mon, 29 Jun 2020 23:21:46: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:21:46: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:21:46: #1 total tags in treatment: 13700752 INFO @ Mon, 29 Jun 2020 23:21:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:21:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:21:46: #1 tags after filtering in treatment: 13700752 INFO @ Mon, 29 Jun 2020 23:21:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:21:46: #1 finished! INFO @ Mon, 29 Jun 2020 23:21:46: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:21:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:21:47: 10000000 INFO @ Mon, 29 Jun 2020 23:21:47: #2 number of paired peaks: 353 WARNING @ Mon, 29 Jun 2020 23:21:47: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 29 Jun 2020 23:21:47: start model_add_line... INFO @ Mon, 29 Jun 2020 23:21:47: start X-correlation... INFO @ Mon, 29 Jun 2020 23:21:47: end of X-cor INFO @ Mon, 29 Jun 2020 23:21:47: #2 finished! INFO @ Mon, 29 Jun 2020 23:21:47: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:21:47: #2 alternative fragment length(s) may be 2,45,541,578 bps INFO @ Mon, 29 Jun 2020 23:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.05_model.r WARNING @ Mon, 29 Jun 2020 23:21:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:21:47: #2 You may need to consider one of the other alternative d(s): 2,45,541,578 WARNING @ Mon, 29 Jun 2020 23:21:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:21:47: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:21:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:21:51: 6000000 INFO @ Mon, 29 Jun 2020 23:21:53: 11000000 INFO @ Mon, 29 Jun 2020 23:21:57: 7000000 INFO @ Mon, 29 Jun 2020 23:22:00: 12000000 INFO @ Mon, 29 Jun 2020 23:22:03: 8000000 INFO @ Mon, 29 Jun 2020 23:22:06: 13000000 INFO @ Mon, 29 Jun 2020 23:22:09: 9000000 INFO @ Mon, 29 Jun 2020 23:22:11: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:22:11: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:22:11: #1 total tags in treatment: 13700752 INFO @ Mon, 29 Jun 2020 23:22:11: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:22:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:22:11: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:22:11: #1 tags after filtering in treatment: 13700752 INFO @ Mon, 29 Jun 2020 23:22:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:22:11: #1 finished! INFO @ Mon, 29 Jun 2020 23:22:11: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:22:12: #2 number of paired peaks: 353 WARNING @ Mon, 29 Jun 2020 23:22:12: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 29 Jun 2020 23:22:12: start model_add_line... INFO @ Mon, 29 Jun 2020 23:22:12: start X-correlation... INFO @ Mon, 29 Jun 2020 23:22:12: end of X-cor INFO @ Mon, 29 Jun 2020 23:22:12: #2 finished! INFO @ Mon, 29 Jun 2020 23:22:12: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:22:12: #2 alternative fragment length(s) may be 2,45,541,578 bps INFO @ Mon, 29 Jun 2020 23:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.10_model.r WARNING @ Mon, 29 Jun 2020 23:22:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:22:12: #2 You may need to consider one of the other alternative d(s): 2,45,541,578 WARNING @ Mon, 29 Jun 2020 23:22:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:22:12: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:22:12: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:22:15: 10000000 INFO @ Mon, 29 Jun 2020 23:22:21: 11000000 INFO @ Mon, 29 Jun 2020 23:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.05_summits.bed INFO @ Mon, 29 Jun 2020 23:22:23: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:22:27: 12000000 INFO @ Mon, 29 Jun 2020 23:22:33: 13000000 INFO @ Mon, 29 Jun 2020 23:22:37: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:22:38: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:22:38: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:22:38: #1 total tags in treatment: 13700752 INFO @ Mon, 29 Jun 2020 23:22:38: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:22:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:22:38: #1 tags after filtering in treatment: 13700752 INFO @ Mon, 29 Jun 2020 23:22:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:22:38: #1 finished! INFO @ Mon, 29 Jun 2020 23:22:38: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:22:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:22:39: #2 number of paired peaks: 353 WARNING @ Mon, 29 Jun 2020 23:22:39: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Mon, 29 Jun 2020 23:22:39: start model_add_line... INFO @ Mon, 29 Jun 2020 23:22:39: start X-correlation... INFO @ Mon, 29 Jun 2020 23:22:39: end of X-cor INFO @ Mon, 29 Jun 2020 23:22:39: #2 finished! INFO @ Mon, 29 Jun 2020 23:22:39: #2 predicted fragment length is 2 bps INFO @ Mon, 29 Jun 2020 23:22:39: #2 alternative fragment length(s) may be 2,45,541,578 bps INFO @ Mon, 29 Jun 2020 23:22:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.20_model.r WARNING @ Mon, 29 Jun 2020 23:22:39: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:22:39: #2 You may need to consider one of the other alternative d(s): 2,45,541,578 WARNING @ Mon, 29 Jun 2020 23:22:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:22:39: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:22:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:22:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:22:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:22:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.10_summits.bed INFO @ Mon, 29 Jun 2020 23:22:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:23:04: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335516/SRX335516.20_summits.bed INFO @ Mon, 29 Jun 2020 23:23:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling