Job ID = 14167028 SRX = SRX8574263 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23906875 spots for SRR12045584/SRR12045584.sra Written 23906875 spots for SRR12045584/SRR12045584.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167380 ("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: 00:04:21 23906875 reads; of these: 23906875 (100.00%) were unpaired; of these: 17865876 (74.73%) aligned 0 times 3176400 (13.29%) aligned exactly 1 time 2864599 (11.98%) aligned >1 times 25.27% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 2453901 / 6040999 = 0.4062 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 09:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.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 09:02:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:02:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:02:12: 1000000 INFO @ Fri, 10 Dec 2021 09:02:24: 2000000 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 09:02:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.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 09:02:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:02:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:02:36: 3000000 INFO @ Fri, 10 Dec 2021 09:02:38: 1000000 INFO @ Fri, 10 Dec 2021 09:02:43: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:02:43: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:02:43: #1 total tags in treatment: 3587098 INFO @ Fri, 10 Dec 2021 09:02:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:02:43: #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 09:02:43: #1 tags after filtering in treatment: 3587098 INFO @ Fri, 10 Dec 2021 09:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:02:43: #1 finished! INFO @ Fri, 10 Dec 2021 09:02:43: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:02:43: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 09:02:43: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 09:02:43: start model_add_line... INFO @ Fri, 10 Dec 2021 09:02:43: start X-correlation... INFO @ Fri, 10 Dec 2021 09:02:43: end of X-cor INFO @ Fri, 10 Dec 2021 09:02:43: #2 finished! INFO @ Fri, 10 Dec 2021 09:02:43: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 09:02:43: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 09:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.05_model.r WARNING @ Fri, 10 Dec 2021 09:02:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:02:43: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 09:02:43: #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 09:02:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:02:46: 2000000 INFO @ Fri, 10 Dec 2021 09:02:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:02:55: 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 09:02:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.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 09:02:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:02:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:02:59: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:02:59: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:02:59: #1 total tags in treatment: 3587098 INFO @ Fri, 10 Dec 2021 09:02:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:02:59: #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 09:02:59: #1 tags after filtering in treatment: 3587098 INFO @ Fri, 10 Dec 2021 09:02:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:02:59: #1 finished! INFO @ Fri, 10 Dec 2021 09:02:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:02:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.05_summits.bed INFO @ Fri, 10 Dec 2021 09:03:00: Done! INFO @ Fri, 10 Dec 2021 09:03:00: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 09:03:00: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 09:03:00: start model_add_line... INFO @ Fri, 10 Dec 2021 09:03:00: start X-correlation... INFO @ Fri, 10 Dec 2021 09:03:00: end of X-cor INFO @ Fri, 10 Dec 2021 09:03:00: #2 finished! INFO @ Fri, 10 Dec 2021 09:03:00: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 09:03:00: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 09:03:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.10_model.r WARNING @ Fri, 10 Dec 2021 09:03:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:03:00: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 09:03:00: #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 09:03:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:03:00: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1057 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:03:07: 1000000 INFO @ Fri, 10 Dec 2021 09:03:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:03:16: 2000000 INFO @ Fri, 10 Dec 2021 09:03:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:03:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:03:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.10_summits.bed INFO @ Fri, 10 Dec 2021 09:03:16: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:03:24: 3000000 INFO @ Fri, 10 Dec 2021 09:03:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 09:03:29: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 09:03:29: #1 total tags in treatment: 3587098 INFO @ Fri, 10 Dec 2021 09:03:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:03:29: #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 09:03:29: #1 tags after filtering in treatment: 3587098 INFO @ Fri, 10 Dec 2021 09:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:03:29: #1 finished! INFO @ Fri, 10 Dec 2021 09:03:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:03:29: #2 number of paired peaks: 259 WARNING @ Fri, 10 Dec 2021 09:03:29: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 10 Dec 2021 09:03:29: start model_add_line... INFO @ Fri, 10 Dec 2021 09:03:29: start X-correlation... INFO @ Fri, 10 Dec 2021 09:03:29: end of X-cor INFO @ Fri, 10 Dec 2021 09:03:29: #2 finished! INFO @ Fri, 10 Dec 2021 09:03:29: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 09:03:29: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 09:03:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.20_model.r WARNING @ Fri, 10 Dec 2021 09:03:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:03:29: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 09:03:29: #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 09:03:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:03:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 09:03:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8574263/SRX8574263.20_summits.bed INFO @ Fri, 10 Dec 2021 09:03:45: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 3 millis CompletedMACS2peakCalling