Job ID = 6626550 SRX = SRX6813087 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9429437 spots for SRR10080055/SRR10080055.sra Written 9429437 spots for SRR10080055/SRR10080055.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626676 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:27 9429437 reads; of these: 9429437 (100.00%) were unpaired; of these: 2016774 (21.39%) aligned 0 times 5831619 (61.84%) aligned exactly 1 time 1581044 (16.77%) aligned >1 times 78.61% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 1269518 / 7412663 = 0.1713 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 @ Tue, 14 Jul 2020 07:34:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.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 @ Tue, 14 Jul 2020 07:34:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:34:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:34:53: 1000000 INFO @ Tue, 14 Jul 2020 07:35:00: 2000000 INFO @ Tue, 14 Jul 2020 07:35:07: 3000000 INFO @ Tue, 14 Jul 2020 07:35:14: 4000000 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 @ Tue, 14 Jul 2020 07:35:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.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 @ Tue, 14 Jul 2020 07:35:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:35:22: 5000000 INFO @ Tue, 14 Jul 2020 07:35:24: 1000000 INFO @ Tue, 14 Jul 2020 07:35:29: 6000000 INFO @ Tue, 14 Jul 2020 07:35:30: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:35:30: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:35:30: #1 total tags in treatment: 6143145 INFO @ Tue, 14 Jul 2020 07:35:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:35:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:35:30: #1 tags after filtering in treatment: 6143145 INFO @ Tue, 14 Jul 2020 07:35:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:35:30: #1 finished! INFO @ Tue, 14 Jul 2020 07:35:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:35:31: #2 number of paired peaks: 117 WARNING @ Tue, 14 Jul 2020 07:35:31: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 14 Jul 2020 07:35:31: start model_add_line... INFO @ Tue, 14 Jul 2020 07:35:31: start X-correlation... INFO @ Tue, 14 Jul 2020 07:35:31: end of X-cor INFO @ Tue, 14 Jul 2020 07:35:31: #2 finished! INFO @ Tue, 14 Jul 2020 07:35:31: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 07:35:31: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 14 Jul 2020 07:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.05_model.r WARNING @ Tue, 14 Jul 2020 07:35:31: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:35:31: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 14 Jul 2020 07:35:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:35:31: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:35:32: 2000000 INFO @ Tue, 14 Jul 2020 07:35:39: 3000000 INFO @ Tue, 14 Jul 2020 07:35:43: #3 Call peaks for each chromosome... 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 @ Tue, 14 Jul 2020 07:35:46: 4000000 INFO @ Tue, 14 Jul 2020 07:35:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.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 @ Tue, 14 Jul 2020 07:35:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:35:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:35:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:35:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.05_summits.bed INFO @ Tue, 14 Jul 2020 07:35:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1012 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:35:53: 5000000 INFO @ Tue, 14 Jul 2020 07:35:54: 1000000 INFO @ Tue, 14 Jul 2020 07:36:01: 2000000 INFO @ Tue, 14 Jul 2020 07:36:03: 6000000 INFO @ Tue, 14 Jul 2020 07:36:04: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:36:04: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:36:04: #1 total tags in treatment: 6143145 INFO @ Tue, 14 Jul 2020 07:36:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:36:04: #1 tags after filtering in treatment: 6143145 INFO @ Tue, 14 Jul 2020 07:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:04: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:05: #2 number of paired peaks: 117 WARNING @ Tue, 14 Jul 2020 07:36:05: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 14 Jul 2020 07:36:05: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:05: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:05: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:05: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:05: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 07:36:05: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 14 Jul 2020 07:36:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.10_model.r WARNING @ Tue, 14 Jul 2020 07:36:05: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:36:05: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 14 Jul 2020 07:36:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:36:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:36:08: 3000000 INFO @ Tue, 14 Jul 2020 07:36:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:36:17: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:36:21: 5000000 INFO @ Tue, 14 Jul 2020 07:36:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.10_summits.bed INFO @ Tue, 14 Jul 2020 07:36:24: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:36:27: 6000000 INFO @ Tue, 14 Jul 2020 07:36:28: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:36:28: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:36:28: #1 total tags in treatment: 6143145 INFO @ Tue, 14 Jul 2020 07:36:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:36:28: #1 tags after filtering in treatment: 6143145 INFO @ Tue, 14 Jul 2020 07:36:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:28: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:29: #2 number of paired peaks: 117 WARNING @ Tue, 14 Jul 2020 07:36:29: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 14 Jul 2020 07:36:29: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:29: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:29: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:29: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:29: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 07:36:29: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 14 Jul 2020 07:36:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.20_model.r WARNING @ Tue, 14 Jul 2020 07:36:29: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:36:29: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 14 Jul 2020 07:36:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:36:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:36:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813087/SRX6813087.20_summits.bed INFO @ Tue, 14 Jul 2020 07:36:47: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 20 millis CompletedMACS2peakCalling