Job ID = 14167185 SRX = SRX11541636 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-10T01:49:08 prefetch.2.10.7: 1) Downloading 'SRR15235734'... 2021-12-10T01:49:08 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T01:51:03 prefetch.2.10.7: HTTPS download succeed 2021-12-10T01:51:03 prefetch.2.10.7: 1) 'SRR15235734' was downloaded successfully 2021-12-10T01:51:03 prefetch.2.10.7: 'SRR15235734' has 0 unresolved dependencies Read 27522041 spots for SRR15235734/SRR15235734.sra Written 27522041 spots for SRR15235734/SRR15235734.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167771 ("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: 00:18:47 27522041 reads; of these: 27522041 (100.00%) were unpaired; of these: 18074862 (65.67%) aligned 0 times 7076475 (25.71%) aligned exactly 1 time 2370704 (8.61%) aligned >1 times 34.33% overall alignment rate Time searching: 00:18:47 Overall time: 00:18:47 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] 5897151 / 9447179 = 0.6242 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.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, 10 Dec 2021 11:14:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:14:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:14:59: 1000000 INFO @ Fri, 10 Dec 2021 11:15:07: 2000000 INFO @ Fri, 10 Dec 2021 11:15:14: 3000000 INFO @ Fri, 10 Dec 2021 11:15:19: #1 tag size is determined as 101 bps INFO @ Fri, 10 Dec 2021 11:15:19: #1 tag size = 101 INFO @ Fri, 10 Dec 2021 11:15:19: #1 total tags in treatment: 3550028 INFO @ Fri, 10 Dec 2021 11:15:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:15:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:15:19: #1 tags after filtering in treatment: 3550028 INFO @ Fri, 10 Dec 2021 11:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:15:19: #1 finished! INFO @ Fri, 10 Dec 2021 11:15:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:15:19: #2 number of paired peaks: 365 WARNING @ Fri, 10 Dec 2021 11:15:19: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Fri, 10 Dec 2021 11:15:19: start model_add_line... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:15:19: start X-correlation... INFO @ Fri, 10 Dec 2021 11:15:19: end of X-cor INFO @ Fri, 10 Dec 2021 11:15:19: #2 finished! INFO @ Fri, 10 Dec 2021 11:15:19: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 11:15:19: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 11:15:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.05_model.r WARNING @ Fri, 10 Dec 2021 11:15:19: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:15:19: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 11:15:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:15:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:15:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.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, 10 Dec 2021 11:15:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:15:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:15:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:15:30: 1000000 INFO @ Fri, 10 Dec 2021 11:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.05_summits.bed INFO @ Fri, 10 Dec 2021 11:15:31: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1029 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:15:38: 2000000 INFO @ Fri, 10 Dec 2021 11:15:46: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 11:15:50: #1 tag size is determined as 101 bps INFO @ Fri, 10 Dec 2021 11:15:50: #1 tag size = 101 INFO @ Fri, 10 Dec 2021 11:15:50: #1 total tags in treatment: 3550028 INFO @ Fri, 10 Dec 2021 11:15:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:15:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:15:50: #1 tags after filtering in treatment: 3550028 INFO @ Fri, 10 Dec 2021 11:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:15:50: #1 finished! INFO @ Fri, 10 Dec 2021 11:15:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:15:51: #2 number of paired peaks: 365 WARNING @ Fri, 10 Dec 2021 11:15:51: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Fri, 10 Dec 2021 11:15:51: start model_add_line... INFO @ Fri, 10 Dec 2021 11:15:51: start X-correlation... INFO @ Fri, 10 Dec 2021 11:15:51: end of X-cor INFO @ Fri, 10 Dec 2021 11:15:51: #2 finished! INFO @ Fri, 10 Dec 2021 11:15:51: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 11:15:51: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 11:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.10_model.r WARNING @ Fri, 10 Dec 2021 11:15:51: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:15:51: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 11:15:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:15:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:15:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.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, 10 Dec 2021 11:15:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:15:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:15:58: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:16:00: 1000000 INFO @ Fri, 10 Dec 2021 11:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.10_summits.bed INFO @ Fri, 10 Dec 2021 11:16:02: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (575 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:16:09: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:16:18: 3000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:16:24: #1 tag size is determined as 101 bps INFO @ Fri, 10 Dec 2021 11:16:24: #1 tag size = 101 INFO @ Fri, 10 Dec 2021 11:16:24: #1 total tags in treatment: 3550028 INFO @ Fri, 10 Dec 2021 11:16:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:16:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:16:24: #1 tags after filtering in treatment: 3550028 INFO @ Fri, 10 Dec 2021 11:16:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:16:24: #1 finished! INFO @ Fri, 10 Dec 2021 11:16:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:16:24: #2 number of paired peaks: 365 WARNING @ Fri, 10 Dec 2021 11:16:24: Fewer paired peaks (365) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 365 pairs to build model! INFO @ Fri, 10 Dec 2021 11:16:24: start model_add_line... INFO @ Fri, 10 Dec 2021 11:16:24: start X-correlation... INFO @ Fri, 10 Dec 2021 11:16:24: end of X-cor INFO @ Fri, 10 Dec 2021 11:16:24: #2 finished! INFO @ Fri, 10 Dec 2021 11:16:24: #2 predicted fragment length is 90 bps INFO @ Fri, 10 Dec 2021 11:16:24: #2 alternative fragment length(s) may be 90 bps INFO @ Fri, 10 Dec 2021 11:16:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.20_model.r WARNING @ Fri, 10 Dec 2021 11:16:24: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:16:24: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Fri, 10 Dec 2021 11:16:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:16:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:16:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:16:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:16:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:16:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:16:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11541636/SRX11541636.20_summits.bed INFO @ Fri, 10 Dec 2021 11:16:36: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (399 records, 4 fields): 2 millis CompletedMACS2peakCalling