Job ID = 6527458 SRX = SRX013082 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:51:39 prefetch.2.10.7: 1) Downloading 'SRR030348'... 2020-06-29T12:51:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:52:52 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:52:52 prefetch.2.10.7: 'SRR030348' is valid 2020-06-29T12:52:52 prefetch.2.10.7: 1) 'SRR030348' was downloaded successfully Read 8682689 spots for SRR030348/SRR030348.sra Written 8682689 spots for SRR030348/SRR030348.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: 00:02:07 8682689 reads; of these: 8682689 (100.00%) were unpaired; of these: 1835275 (21.14%) aligned 0 times 5682225 (65.44%) aligned exactly 1 time 1165189 (13.42%) aligned >1 times 78.86% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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_rmdupse_core] 697588 / 6847414 = 0.1019 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 21:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.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 21:58:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:58:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:59:02: 1000000 INFO @ Mon, 29 Jun 2020 21:59:08: 2000000 INFO @ Mon, 29 Jun 2020 21:59:13: 3000000 INFO @ Mon, 29 Jun 2020 21:59:18: 4000000 INFO @ Mon, 29 Jun 2020 21:59:24: 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 @ Mon, 29 Jun 2020 21:59:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.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 21:59:27: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:59:27: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:59:29: 6000000 INFO @ Mon, 29 Jun 2020 21:59:30: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:59:30: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:59:30: #1 total tags in treatment: 6149826 INFO @ Mon, 29 Jun 2020 21:59:30: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:59:30: #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 21:59:30: #1 tags after filtering in treatment: 6149826 INFO @ Mon, 29 Jun 2020 21:59:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:59:30: #1 finished! INFO @ Mon, 29 Jun 2020 21:59:30: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:59:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:59:31: #2 number of paired peaks: 112 WARNING @ Mon, 29 Jun 2020 21:59:31: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 29 Jun 2020 21:59:31: start model_add_line... INFO @ Mon, 29 Jun 2020 21:59:31: start X-correlation... INFO @ Mon, 29 Jun 2020 21:59:31: end of X-cor INFO @ Mon, 29 Jun 2020 21:59:31: #2 finished! INFO @ Mon, 29 Jun 2020 21:59:31: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 21:59:31: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 21:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.05_model.r WARNING @ Mon, 29 Jun 2020 21:59:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:59:31: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 21:59:31: #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 21:59:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:59:33: 1000000 INFO @ Mon, 29 Jun 2020 21:59:39: 2000000 INFO @ Mon, 29 Jun 2020 21:59:44: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:59:44: 3000000 INFO @ Mon, 29 Jun 2020 21:59:50: 4000000 INFO @ Mon, 29 Jun 2020 21:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.05_summits.bed INFO @ Mon, 29 Jun 2020 21:59:51: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Mon, 29 Jun 2020 21:59:55: 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 @ Mon, 29 Jun 2020 21:59:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.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 21:59:57: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:59:57: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:00:01: 6000000 INFO @ Mon, 29 Jun 2020 22:00:02: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:00:02: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:00:02: #1 total tags in treatment: 6149826 INFO @ Mon, 29 Jun 2020 22:00:02: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:00:02: #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 22:00:02: #1 tags after filtering in treatment: 6149826 INFO @ Mon, 29 Jun 2020 22:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:00:02: #1 finished! INFO @ Mon, 29 Jun 2020 22:00:02: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:00:03: #2 number of paired peaks: 112 WARNING @ Mon, 29 Jun 2020 22:00:03: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 29 Jun 2020 22:00:03: start model_add_line... INFO @ Mon, 29 Jun 2020 22:00:03: start X-correlation... INFO @ Mon, 29 Jun 2020 22:00:03: end of X-cor INFO @ Mon, 29 Jun 2020 22:00:03: #2 finished! INFO @ Mon, 29 Jun 2020 22:00:03: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 22:00:03: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 22:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.10_model.r WARNING @ Mon, 29 Jun 2020 22:00:03: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:00:03: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 22:00:03: #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 22:00:03: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:00:04: 1000000 INFO @ Mon, 29 Jun 2020 22:00:10: 2000000 INFO @ Mon, 29 Jun 2020 22:00:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:00:16: 3000000 INFO @ Mon, 29 Jun 2020 22:00:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.10_summits.bed INFO @ Mon, 29 Jun 2020 22:00:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (772 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:00:23: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:00:29: 5000000 INFO @ Mon, 29 Jun 2020 22:00:36: 6000000 INFO @ Mon, 29 Jun 2020 22:00:36: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:00:36: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:00:36: #1 total tags in treatment: 6149826 INFO @ Mon, 29 Jun 2020 22:00:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:00:36: #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 22:00:37: #1 tags after filtering in treatment: 6149826 INFO @ Mon, 29 Jun 2020 22:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:00:37: #1 finished! INFO @ Mon, 29 Jun 2020 22:00:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:00:37: #2 number of paired peaks: 112 WARNING @ Mon, 29 Jun 2020 22:00:37: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 29 Jun 2020 22:00:37: start model_add_line... INFO @ Mon, 29 Jun 2020 22:00:37: start X-correlation... INFO @ Mon, 29 Jun 2020 22:00:37: end of X-cor INFO @ Mon, 29 Jun 2020 22:00:37: #2 finished! INFO @ Mon, 29 Jun 2020 22:00:37: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 22:00:37: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 22:00:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.20_model.r WARNING @ Mon, 29 Jun 2020 22:00:37: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:00:37: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 22:00:37: #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 22:00:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:00:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:00:50: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:00:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:00:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:00:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX013082/SRX013082.20_summits.bed INFO @ Mon, 29 Jun 2020 22:00:57: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (359 records, 4 fields): 2 millis CompletedMACS2peakCalling