Job ID = 6455647 SRX = SRX287955 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:08:51 prefetch.2.10.7: 1) Downloading 'SRR870144'... 2020-06-21T10:08:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:10:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:10:35 prefetch.2.10.7: 'SRR870144' is valid 2020-06-21T10:10:35 prefetch.2.10.7: 1) 'SRR870144' was downloaded successfully Read 14616808 spots for SRR870144/SRR870144.sra Written 14616808 spots for SRR870144/SRR870144.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: 00:04:18 14616808 reads; of these: 14616808 (100.00%) were unpaired; of these: 1026280 (7.02%) aligned 0 times 9725946 (66.54%) aligned exactly 1 time 3864582 (26.44%) aligned >1 times 92.98% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 4043938 / 13590528 = 0.2976 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 19:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.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 19:19:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:10: 1000000 INFO @ Sun, 21 Jun 2020 19:19:16: 2000000 INFO @ Sun, 21 Jun 2020 19:19:22: 3000000 INFO @ Sun, 21 Jun 2020 19:19:28: 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 19:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.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 19:19:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:33: 5000000 INFO @ Sun, 21 Jun 2020 19:19:40: 6000000 INFO @ Sun, 21 Jun 2020 19:19:40: 1000000 INFO @ Sun, 21 Jun 2020 19:19:47: 7000000 INFO @ Sun, 21 Jun 2020 19:19:47: 2000000 INFO @ Sun, 21 Jun 2020 19:19:54: 3000000 INFO @ Sun, 21 Jun 2020 19:19:54: 8000000 INFO @ Sun, 21 Jun 2020 19:20:01: 4000000 INFO @ Sun, 21 Jun 2020 19:20:01: 9000000 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 19:20:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.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 19:20:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:20:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:20:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:05: #1 total tags in treatment: 9546590 INFO @ Sun, 21 Jun 2020 19:20:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:05: #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 19:20:05: #1 tags after filtering in treatment: 9546586 INFO @ Sun, 21 Jun 2020 19:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:06: #2 number of paired peaks: 404 WARNING @ Sun, 21 Jun 2020 19:20:06: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Sun, 21 Jun 2020 19:20:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:06: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:20:06: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 19:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.05_model.r WARNING @ Sun, 21 Jun 2020 19:20:06: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:20:06: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 19:20:06: #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 19:20:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:20:08: 5000000 INFO @ Sun, 21 Jun 2020 19:20:10: 1000000 INFO @ Sun, 21 Jun 2020 19:20:14: 6000000 INFO @ Sun, 21 Jun 2020 19:20:17: 2000000 INFO @ Sun, 21 Jun 2020 19:20:21: 7000000 INFO @ Sun, 21 Jun 2020 19:20:23: 3000000 INFO @ Sun, 21 Jun 2020 19:20:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:20:28: 8000000 INFO @ Sun, 21 Jun 2020 19:20:30: 4000000 INFO @ Sun, 21 Jun 2020 19:20:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.05_summits.bed INFO @ Sun, 21 Jun 2020 19:20:35: Done! pass1 - making usageList (664 chroms): 1 millis pass2 - checking and writing primary data (2278 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:20:35: 9000000 INFO @ Sun, 21 Jun 2020 19:20:37: 5000000 INFO @ Sun, 21 Jun 2020 19:20:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:39: #1 total tags in treatment: 9546590 INFO @ Sun, 21 Jun 2020 19:20:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:39: #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 19:20:39: #1 tags after filtering in treatment: 9546586 INFO @ Sun, 21 Jun 2020 19:20:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:40: #2 number of paired peaks: 404 WARNING @ Sun, 21 Jun 2020 19:20:40: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Sun, 21 Jun 2020 19:20:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:40: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:20:40: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 19:20:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.10_model.r WARNING @ Sun, 21 Jun 2020 19:20:40: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:20:40: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 19:20:40: #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 19:20:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:20:43: 6000000 INFO @ Sun, 21 Jun 2020 19:20:50: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:20:56: 8000000 INFO @ Sun, 21 Jun 2020 19:20:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:21:03: 9000000 INFO @ Sun, 21 Jun 2020 19:21:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:21:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:21:06: #1 total tags in treatment: 9546590 INFO @ Sun, 21 Jun 2020 19:21:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:21:06: #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 19:21:07: #1 tags after filtering in treatment: 9546586 INFO @ Sun, 21 Jun 2020 19:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:21:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:21:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:21:07: #2 number of paired peaks: 404 WARNING @ Sun, 21 Jun 2020 19:21:07: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Sun, 21 Jun 2020 19:21:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:21:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:21:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:21:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:21:07: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:21:07: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 19:21:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.20_model.r WARNING @ Sun, 21 Jun 2020 19:21:07: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:21:07: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 19:21:07: #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 19:21:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.10_summits.bed INFO @ Sun, 21 Jun 2020 19:21:09: Done! pass1 - making usageList (426 chroms): 1 millis pass2 - checking and writing primary data (1037 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:21:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:21:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287955/SRX287955.20_summits.bed INFO @ Sun, 21 Jun 2020 19:21:36: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 6 millis CompletedMACS2peakCalling