Job ID = 6452935 SRX = SRX050601 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:49:15 prefetch.2.10.7: 1) Downloading 'SRR139083'... 2020-06-21T07:49:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:50:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:50:14 prefetch.2.10.7: 'SRR139083' is valid 2020-06-21T07:50:14 prefetch.2.10.7: 1) 'SRR139083' was downloaded successfully Read 6948791 spots for SRR139083/SRR139083.sra Written 6948791 spots for SRR139083/SRR139083.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: 00:01:29 6948791 reads; of these: 6948791 (100.00%) were unpaired; of these: 302189 (4.35%) aligned 0 times 4941205 (71.11%) aligned exactly 1 time 1705397 (24.54%) aligned >1 times 95.65% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 412856 / 6646602 = 0.0621 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 16:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.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 16:53:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:53:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:53:56: 1000000 INFO @ Sun, 21 Jun 2020 16:54:00: 2000000 INFO @ Sun, 21 Jun 2020 16:54:05: 3000000 INFO @ Sun, 21 Jun 2020 16:54:09: 4000000 INFO @ Sun, 21 Jun 2020 16:54:14: 5000000 INFO @ Sun, 21 Jun 2020 16:54:18: 6000000 INFO @ Sun, 21 Jun 2020 16:54:19: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:54:19: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:54:19: #1 total tags in treatment: 6233746 INFO @ Sun, 21 Jun 2020 16:54:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 16:54:20: #1 tags after filtering in treatment: 6233739 INFO @ Sun, 21 Jun 2020 16:54:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:20: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:20: #2 number of paired peaks: 434 WARNING @ Sun, 21 Jun 2020 16:54:20: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 21 Jun 2020 16:54:20: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:20: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:20: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:20: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:20: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 16:54:20: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 16:54:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.05_model.r WARNING @ Sun, 21 Jun 2020 16:54:20: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:54:20: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 16:54:20: #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 16:54:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.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 16:54:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:54:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:54:26: 1000000 INFO @ Sun, 21 Jun 2020 16:54:30: 2000000 INFO @ Sun, 21 Jun 2020 16:54:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:54:35: 3000000 INFO @ Sun, 21 Jun 2020 16:54:39: 4000000 INFO @ Sun, 21 Jun 2020 16:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.05_summits.bed INFO @ Sun, 21 Jun 2020 16:54:40: Done! pass1 - making usageList (489 chroms): 1 millis pass2 - checking and writing primary data (1501 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:54:44: 5000000 INFO @ Sun, 21 Jun 2020 16:54:48: 6000000 INFO @ Sun, 21 Jun 2020 16:54:50: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:54:50: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:54:50: #1 total tags in treatment: 6233746 INFO @ Sun, 21 Jun 2020 16:54:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:54:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 16:54:50: #1 tags after filtering in treatment: 6233739 INFO @ Sun, 21 Jun 2020 16:54:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:54:50: #1 finished! INFO @ Sun, 21 Jun 2020 16:54:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:54:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:54:50: #2 number of paired peaks: 434 WARNING @ Sun, 21 Jun 2020 16:54:50: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 21 Jun 2020 16:54:50: start model_add_line... INFO @ Sun, 21 Jun 2020 16:54:50: start X-correlation... INFO @ Sun, 21 Jun 2020 16:54:51: end of X-cor INFO @ Sun, 21 Jun 2020 16:54:51: #2 finished! INFO @ Sun, 21 Jun 2020 16:54:51: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 16:54:51: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 16:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.10_model.r WARNING @ Sun, 21 Jun 2020 16:54:51: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:54:51: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 16:54:51: #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 16:54:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.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 16:54:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:54:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:54:56: 1000000 INFO @ Sun, 21 Jun 2020 16:55:00: 2000000 INFO @ Sun, 21 Jun 2020 16:55:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:55:05: 3000000 INFO @ Sun, 21 Jun 2020 16:55:09: 4000000 INFO @ Sun, 21 Jun 2020 16:55:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.10_summits.bed INFO @ Sun, 21 Jun 2020 16:55:10: Done! pass1 - making usageList (189 chroms): 0 millis pass2 - checking and writing primary data (380 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:55:14: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:55:19: 6000000 INFO @ Sun, 21 Jun 2020 16:55:20: #1 tag size is determined as 30 bps INFO @ Sun, 21 Jun 2020 16:55:20: #1 tag size = 30 INFO @ Sun, 21 Jun 2020 16:55:20: #1 total tags in treatment: 6233746 INFO @ Sun, 21 Jun 2020 16:55:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:55:20: #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 16:55:20: #1 tags after filtering in treatment: 6233739 INFO @ Sun, 21 Jun 2020 16:55:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:55:20: #1 finished! INFO @ Sun, 21 Jun 2020 16:55:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:55:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:55:21: #2 number of paired peaks: 434 WARNING @ Sun, 21 Jun 2020 16:55:21: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Sun, 21 Jun 2020 16:55:21: start model_add_line... INFO @ Sun, 21 Jun 2020 16:55:21: start X-correlation... INFO @ Sun, 21 Jun 2020 16:55:21: end of X-cor INFO @ Sun, 21 Jun 2020 16:55:21: #2 finished! INFO @ Sun, 21 Jun 2020 16:55:21: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 16:55:21: #2 alternative fragment length(s) may be 45 bps INFO @ Sun, 21 Jun 2020 16:55:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.20_model.r WARNING @ Sun, 21 Jun 2020 16:55:21: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:55:21: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sun, 21 Jun 2020 16:55:21: #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 16:55:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:55:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:55:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX050601/SRX050601.20_summits.bed INFO @ Sun, 21 Jun 2020 16:55:40: Done! pass1 - making usageList (79 chroms): 0 millis pass2 - checking and writing primary data (155 records, 4 fields): 4 millis CompletedMACS2peakCalling