Job ID = 6528346 SRX = SRX5360598 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:50:25 prefetch.2.10.7: 1) Downloading 'SRR8559074'... 2020-06-29T14:50:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:50:41 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:50:41 prefetch.2.10.7: 'SRR8559074' is valid 2020-06-29T14:50:41 prefetch.2.10.7: 1) 'SRR8559074' was downloaded successfully Read 250993 spots for SRR8559074/SRR8559074.sra Written 250993 spots for SRR8559074/SRR8559074.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: 00:00:03 250993 reads; of these: 250993 (100.00%) were unpaired; of these: 100512 (40.05%) aligned 0 times 143942 (57.35%) aligned exactly 1 time 6539 (2.61%) aligned >1 times 59.95% overall alignment rate Time searching: 00:00:03 Overall time: 00:00:03 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] 55304 / 150481 = 0.3675 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 23:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.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 23:51:25: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:51:25: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:51:25: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:51:25: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:51:25: #1 total tags in treatment: 95177 INFO @ Mon, 29 Jun 2020 23:51:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:51:25: #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 23:51:25: #1 tags after filtering in treatment: 95174 INFO @ Mon, 29 Jun 2020 23:51:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:51:25: #1 finished! INFO @ Mon, 29 Jun 2020 23:51:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:51:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:51:25: #2 number of paired peaks: 130 WARNING @ Mon, 29 Jun 2020 23:51:25: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Mon, 29 Jun 2020 23:51:25: start model_add_line... INFO @ Mon, 29 Jun 2020 23:51:25: start X-correlation... INFO @ Mon, 29 Jun 2020 23:51:26: end of X-cor INFO @ Mon, 29 Jun 2020 23:51:26: #2 finished! INFO @ Mon, 29 Jun 2020 23:51:26: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:51:26: #2 alternative fragment length(s) may be 47,239,342,385,414,438,458,490,509,566,578 bps INFO @ Mon, 29 Jun 2020 23:51:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.05_model.r WARNING @ Mon, 29 Jun 2020 23:51:26: #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 23:51:26: #2 You may need to consider one of the other alternative d(s): 47,239,342,385,414,438,458,490,509,566,578 WARNING @ Mon, 29 Jun 2020 23:51:26: #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 23:51:26: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:51:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:51:26: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:51:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:51:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:51:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.05_summits.bed INFO @ Mon, 29 Jun 2020 23:51:26: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 1 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 @ Mon, 29 Jun 2020 23:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.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 23:51:55: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:51:55: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:51:56: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:51:56: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:51:56: #1 total tags in treatment: 95177 INFO @ Mon, 29 Jun 2020 23:51:56: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:51:56: #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 23:51:56: #1 tags after filtering in treatment: 95174 INFO @ Mon, 29 Jun 2020 23:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:51:56: #1 finished! INFO @ Mon, 29 Jun 2020 23:51:56: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:51:56: #2 number of paired peaks: 130 WARNING @ Mon, 29 Jun 2020 23:51:56: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Mon, 29 Jun 2020 23:51:56: start model_add_line... INFO @ Mon, 29 Jun 2020 23:51:56: start X-correlation... INFO @ Mon, 29 Jun 2020 23:51:56: end of X-cor INFO @ Mon, 29 Jun 2020 23:51:56: #2 finished! INFO @ Mon, 29 Jun 2020 23:51:56: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:51:56: #2 alternative fragment length(s) may be 47,239,342,385,414,438,458,490,509,566,578 bps INFO @ Mon, 29 Jun 2020 23:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.10_model.r WARNING @ Mon, 29 Jun 2020 23:51:56: #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 23:51:56: #2 You may need to consider one of the other alternative d(s): 47,239,342,385,414,438,458,490,509,566,578 WARNING @ Mon, 29 Jun 2020 23:51:56: #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 23:51:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:51:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:51:56: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:51:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:51:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:51:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.10_summits.bed INFO @ Mon, 29 Jun 2020 23:51:56: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 3 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.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 23:52:25: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:52:25: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:52:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:52:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:52:26: #1 total tags in treatment: 95177 INFO @ Mon, 29 Jun 2020 23:52:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:52:26: #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 23:52:26: #1 tags after filtering in treatment: 95174 INFO @ Mon, 29 Jun 2020 23:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:52:26: #1 finished! INFO @ Mon, 29 Jun 2020 23:52:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:52:26: #2 number of paired peaks: 130 WARNING @ Mon, 29 Jun 2020 23:52:26: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Mon, 29 Jun 2020 23:52:26: start model_add_line... INFO @ Mon, 29 Jun 2020 23:52:26: start X-correlation... INFO @ Mon, 29 Jun 2020 23:52:26: end of X-cor INFO @ Mon, 29 Jun 2020 23:52:26: #2 finished! INFO @ Mon, 29 Jun 2020 23:52:26: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:52:26: #2 alternative fragment length(s) may be 47,239,342,385,414,438,458,490,509,566,578 bps INFO @ Mon, 29 Jun 2020 23:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.20_model.r WARNING @ Mon, 29 Jun 2020 23:52:26: #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 23:52:26: #2 You may need to consider one of the other alternative d(s): 47,239,342,385,414,438,458,490,509,566,578 WARNING @ Mon, 29 Jun 2020 23:52:26: #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 23:52:26: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:52:26: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:52:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:52:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:52:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5360598/SRX5360598.20_summits.bed INFO @ Mon, 29 Jun 2020 23:52:26: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling