Job ID = 6509066 SRX = SRX645109 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:57:59 prefetch.2.10.7: 1) Downloading 'SRR1505708'... 2020-06-26T14:57:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:03:43 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:03:43 prefetch.2.10.7: 1) 'SRR1505708' was downloaded successfully Read 33543582 spots for SRR1505708/SRR1505708.sra Written 33543582 spots for SRR1505708/SRR1505708.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: 00:09:58 33543582 reads; of these: 33543582 (100.00%) were unpaired; of these: 25673704 (76.54%) aligned 0 times 6246367 (18.62%) aligned exactly 1 time 1623511 (4.84%) aligned >1 times 23.46% overall alignment rate Time searching: 00:09:58 Overall time: 00:09:58 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_rmdupse_core] 5666051 / 7869878 = 0.7200 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 @ Sat, 27 Jun 2020 00:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.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 @ Sat, 27 Jun 2020 00:18:44: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:18:44: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:18:51: 1000000 INFO @ Sat, 27 Jun 2020 00:18:59: 2000000 INFO @ Sat, 27 Jun 2020 00:19:01: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:19:01: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:19:01: #1 total tags in treatment: 2203827 INFO @ Sat, 27 Jun 2020 00:19:01: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:19:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:19:01: #1 tags after filtering in treatment: 2203721 INFO @ Sat, 27 Jun 2020 00:19:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:19:01: #1 finished! INFO @ Sat, 27 Jun 2020 00:19:01: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:19:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:19:02: #2 number of paired peaks: 989 WARNING @ Sat, 27 Jun 2020 00:19:02: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Sat, 27 Jun 2020 00:19:02: start model_add_line... INFO @ Sat, 27 Jun 2020 00:19:02: start X-correlation... INFO @ Sat, 27 Jun 2020 00:19:02: end of X-cor INFO @ Sat, 27 Jun 2020 00:19:02: #2 finished! INFO @ Sat, 27 Jun 2020 00:19:02: #2 predicted fragment length is 105 bps INFO @ Sat, 27 Jun 2020 00:19:02: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 27 Jun 2020 00:19:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.05_model.r WARNING @ Sat, 27 Jun 2020 00:19:02: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:19:02: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sat, 27 Jun 2020 00:19:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:19:02: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:19:07: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:19:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:19:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:19:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.05_summits.bed INFO @ Sat, 27 Jun 2020 00:19:10: Done! pass1 - making usageList (479 chroms): 1 millis pass2 - checking and writing primary data (1181 records, 4 fields): 27 millis CompletedMACS2peakCalling 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 @ Sat, 27 Jun 2020 00:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.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 @ Sat, 27 Jun 2020 00:19:14: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:19:14: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:19:20: 1000000 INFO @ Sat, 27 Jun 2020 00:19:28: 2000000 INFO @ Sat, 27 Jun 2020 00:19:29: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:19:29: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:19:29: #1 total tags in treatment: 2203827 INFO @ Sat, 27 Jun 2020 00:19:29: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:19:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:19:29: #1 tags after filtering in treatment: 2203721 INFO @ Sat, 27 Jun 2020 00:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:19:29: #1 finished! INFO @ Sat, 27 Jun 2020 00:19:29: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:19:30: #2 number of paired peaks: 989 WARNING @ Sat, 27 Jun 2020 00:19:30: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Sat, 27 Jun 2020 00:19:30: start model_add_line... INFO @ Sat, 27 Jun 2020 00:19:30: start X-correlation... INFO @ Sat, 27 Jun 2020 00:19:30: end of X-cor INFO @ Sat, 27 Jun 2020 00:19:30: #2 finished! INFO @ Sat, 27 Jun 2020 00:19:30: #2 predicted fragment length is 105 bps INFO @ Sat, 27 Jun 2020 00:19:30: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 27 Jun 2020 00:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.10_model.r WARNING @ Sat, 27 Jun 2020 00:19:30: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:19:30: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sat, 27 Jun 2020 00:19:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:19:30: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:19:36: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:19:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:19:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:19:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.10_summits.bed INFO @ Sat, 27 Jun 2020 00:19:39: Done! pass1 - making usageList (283 chroms): 1 millis pass2 - checking and writing primary data (518 records, 4 fields): 10 millis CompletedMACS2peakCalling 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 @ Sat, 27 Jun 2020 00:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.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 @ Sat, 27 Jun 2020 00:19:44: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:19:44: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:19:51: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:19:59: 2000000 INFO @ Sat, 27 Jun 2020 00:20:01: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:20:01: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:20:01: #1 total tags in treatment: 2203827 INFO @ Sat, 27 Jun 2020 00:20:01: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:20:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:20:02: #1 tags after filtering in treatment: 2203721 INFO @ Sat, 27 Jun 2020 00:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:20:02: #1 finished! INFO @ Sat, 27 Jun 2020 00:20:02: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:20:02: #2 number of paired peaks: 989 WARNING @ Sat, 27 Jun 2020 00:20:02: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Sat, 27 Jun 2020 00:20:02: start model_add_line... INFO @ Sat, 27 Jun 2020 00:20:02: start X-correlation... INFO @ Sat, 27 Jun 2020 00:20:02: end of X-cor INFO @ Sat, 27 Jun 2020 00:20:02: #2 finished! INFO @ Sat, 27 Jun 2020 00:20:02: #2 predicted fragment length is 105 bps INFO @ Sat, 27 Jun 2020 00:20:02: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 27 Jun 2020 00:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.20_model.r WARNING @ Sat, 27 Jun 2020 00:20:02: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:20:02: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sat, 27 Jun 2020 00:20:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:20:02: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:20:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:20:08: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:20:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:20:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:20:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645109/SRX645109.20_summits.bed INFO @ Sat, 27 Jun 2020 00:20:10: Done! pass1 - making usageList (101 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 4 millis CompletedMACS2peakCalling