Job ID = 6498699 SRX = SRX706812 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:57:49 prefetch.2.10.7: 1) Downloading 'SRR1581493'... 2020-06-25T23:57:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:59:34 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:59:35 prefetch.2.10.7: 'SRR1581493' is valid 2020-06-25T23:59:35 prefetch.2.10.7: 1) 'SRR1581493' was downloaded successfully Read 17095851 spots for SRR1581493/SRR1581493.sra Written 17095851 spots for SRR1581493/SRR1581493.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: 00:02:57 17095851 reads; of these: 17095851 (100.00%) were unpaired; of these: 10199450 (59.66%) aligned 0 times 5518312 (32.28%) aligned exactly 1 time 1378089 (8.06%) aligned >1 times 40.34% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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] 2988286 / 6896401 = 0.4333 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 @ Fri, 26 Jun 2020 09:05:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.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 @ Fri, 26 Jun 2020 09:05:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:05:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:05:30: 1000000 INFO @ Fri, 26 Jun 2020 09:05:35: 2000000 INFO @ Fri, 26 Jun 2020 09:05:41: 3000000 INFO @ Fri, 26 Jun 2020 09:05:46: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:05:46: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:05:46: #1 total tags in treatment: 3908115 INFO @ Fri, 26 Jun 2020 09:05:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:05:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:05:47: #1 tags after filtering in treatment: 3908115 INFO @ Fri, 26 Jun 2020 09:05:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:05:47: #1 finished! INFO @ Fri, 26 Jun 2020 09:05:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:05:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:05:47: #2 number of paired peaks: 171 WARNING @ Fri, 26 Jun 2020 09:05:47: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 26 Jun 2020 09:05:47: start model_add_line... INFO @ Fri, 26 Jun 2020 09:05:47: start X-correlation... INFO @ Fri, 26 Jun 2020 09:05:47: end of X-cor INFO @ Fri, 26 Jun 2020 09:05:47: #2 finished! INFO @ Fri, 26 Jun 2020 09:05:47: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 09:05:47: #2 alternative fragment length(s) may be 50,510 bps INFO @ Fri, 26 Jun 2020 09:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.05_model.r WARNING @ Fri, 26 Jun 2020 09:05:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:05:47: #2 You may need to consider one of the other alternative d(s): 50,510 WARNING @ Fri, 26 Jun 2020 09:05:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:05:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:05:47: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 09:05:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.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 @ Fri, 26 Jun 2020 09:05:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:05:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:05:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:06:00: 1000000 INFO @ Fri, 26 Jun 2020 09:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.05_summits.bed INFO @ Fri, 26 Jun 2020 09:06:01: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (505 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:06:06: 2000000 INFO @ Fri, 26 Jun 2020 09:06:11: 3000000 INFO @ Fri, 26 Jun 2020 09:06:16: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:06:16: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:06:16: #1 total tags in treatment: 3908115 INFO @ Fri, 26 Jun 2020 09:06:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:06:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:06:17: #1 tags after filtering in treatment: 3908115 INFO @ Fri, 26 Jun 2020 09:06:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:06:17: #1 finished! INFO @ Fri, 26 Jun 2020 09:06:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:06:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:06:17: #2 number of paired peaks: 171 WARNING @ Fri, 26 Jun 2020 09:06:17: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 26 Jun 2020 09:06:17: start model_add_line... INFO @ Fri, 26 Jun 2020 09:06:17: start X-correlation... INFO @ Fri, 26 Jun 2020 09:06:17: end of X-cor INFO @ Fri, 26 Jun 2020 09:06:17: #2 finished! INFO @ Fri, 26 Jun 2020 09:06:17: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 09:06:17: #2 alternative fragment length(s) may be 50,510 bps INFO @ Fri, 26 Jun 2020 09:06:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.10_model.r WARNING @ Fri, 26 Jun 2020 09:06:22: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:06:22: #2 You may need to consider one of the other alternative d(s): 50,510 WARNING @ Fri, 26 Jun 2020 09:06:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:06:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:06:22: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 09:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.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 @ Fri, 26 Jun 2020 09:06:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:06:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:06:30: 1000000 INFO @ Fri, 26 Jun 2020 09:06:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:06:36: 2000000 INFO @ Fri, 26 Jun 2020 09:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:06:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.10_summits.bed INFO @ Fri, 26 Jun 2020 09:06:36: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:06:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:06:47: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:06:47: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:06:47: #1 total tags in treatment: 3908115 INFO @ Fri, 26 Jun 2020 09:06:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:06:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:06:47: #1 tags after filtering in treatment: 3908115 INFO @ Fri, 26 Jun 2020 09:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:06:47: #1 finished! INFO @ Fri, 26 Jun 2020 09:06:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:06:47: #2 number of paired peaks: 171 WARNING @ Fri, 26 Jun 2020 09:06:47: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Fri, 26 Jun 2020 09:06:47: start model_add_line... INFO @ Fri, 26 Jun 2020 09:06:47: start X-correlation... INFO @ Fri, 26 Jun 2020 09:06:47: end of X-cor INFO @ Fri, 26 Jun 2020 09:06:47: #2 finished! INFO @ Fri, 26 Jun 2020 09:06:47: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 09:06:47: #2 alternative fragment length(s) may be 50,510 bps INFO @ Fri, 26 Jun 2020 09:06:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.20_model.r WARNING @ Fri, 26 Jun 2020 09:06:47: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:06:47: #2 You may need to consider one of the other alternative d(s): 50,510 WARNING @ Fri, 26 Jun 2020 09:06:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:06:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:06:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:06:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:07:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:07:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:07:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706812/SRX706812.20_summits.bed INFO @ Fri, 26 Jun 2020 09:07:02: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 1 millis CompletedMACS2peakCalling