Job ID = 12265194 SRX = SRX3426796 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7881898 spots for SRR6327147/SRR6327147.sra Written 7881898 spots for SRR6327147/SRR6327147.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265334 ("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: 00:02:18 7881898 reads; of these: 7881898 (100.00%) were unpaired; of these: 2409988 (30.58%) aligned 0 times 4736374 (60.09%) aligned exactly 1 time 735536 (9.33%) aligned >1 times 69.42% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 1538683 / 5471910 = 0.2812 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:16:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.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 @ Sat, 03 Apr 2021 06:16:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:16:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:16:43: 1000000 INFO @ Sat, 03 Apr 2021 06:16:50: 2000000 INFO @ Sat, 03 Apr 2021 06:16:57: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:17:04: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:17:04: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:17:04: #1 total tags in treatment: 3933227 INFO @ Sat, 03 Apr 2021 06:17:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:17:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:17:04: #1 tags after filtering in treatment: 3933227 INFO @ Sat, 03 Apr 2021 06:17:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:17:04: #1 finished! INFO @ Sat, 03 Apr 2021 06:17:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:17:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:17:05: #2 number of paired peaks: 3911 INFO @ Sat, 03 Apr 2021 06:17:05: start model_add_line... INFO @ Sat, 03 Apr 2021 06:17:05: start X-correlation... INFO @ Sat, 03 Apr 2021 06:17:05: end of X-cor INFO @ Sat, 03 Apr 2021 06:17:05: #2 finished! INFO @ Sat, 03 Apr 2021 06:17:05: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:17:05: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:17:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.05_model.r WARNING @ Sat, 03 Apr 2021 06:17:05: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:17:05: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:17:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:17:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:17:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:17:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.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 @ Sat, 03 Apr 2021 06:17:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:17:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:17:15: 1000000 INFO @ Sat, 03 Apr 2021 06:17:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.05_summits.bed INFO @ Sat, 03 Apr 2021 06:17:23: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (12764 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:17:24: 2000000 INFO @ Sat, 03 Apr 2021 06:17:33: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:17:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.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 @ Sat, 03 Apr 2021 06:17:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:17:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:17:42: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:17:42: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:17:42: #1 total tags in treatment: 3933227 INFO @ Sat, 03 Apr 2021 06:17:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:17:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:17:42: #1 tags after filtering in treatment: 3933227 INFO @ Sat, 03 Apr 2021 06:17:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:17:42: #1 finished! INFO @ Sat, 03 Apr 2021 06:17:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:17:42: #2 number of paired peaks: 3911 INFO @ Sat, 03 Apr 2021 06:17:42: start model_add_line... INFO @ Sat, 03 Apr 2021 06:17:42: start X-correlation... INFO @ Sat, 03 Apr 2021 06:17:42: end of X-cor INFO @ Sat, 03 Apr 2021 06:17:42: #2 finished! INFO @ Sat, 03 Apr 2021 06:17:42: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:17:42: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:17:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.10_model.r WARNING @ Sat, 03 Apr 2021 06:17:42: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:17:42: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:17:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:17:42: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:17:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:17:44: 1000000 INFO @ Sat, 03 Apr 2021 06:17:51: 2000000 INFO @ Sat, 03 Apr 2021 06:17:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:17:59: 3000000 INFO @ Sat, 03 Apr 2021 06:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.10_summits.bed INFO @ Sat, 03 Apr 2021 06:18:00: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6487 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:18:06: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:18:06: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:18:06: #1 total tags in treatment: 3933227 INFO @ Sat, 03 Apr 2021 06:18:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:18:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:18:07: #1 tags after filtering in treatment: 3933227 INFO @ Sat, 03 Apr 2021 06:18:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:18:07: #1 finished! INFO @ Sat, 03 Apr 2021 06:18:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:18:07: #2 number of paired peaks: 3911 INFO @ Sat, 03 Apr 2021 06:18:07: start model_add_line... INFO @ Sat, 03 Apr 2021 06:18:07: start X-correlation... INFO @ Sat, 03 Apr 2021 06:18:07: end of X-cor INFO @ Sat, 03 Apr 2021 06:18:07: #2 finished! INFO @ Sat, 03 Apr 2021 06:18:07: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 06:18:07: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 06:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.20_model.r WARNING @ Sat, 03 Apr 2021 06:18:07: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:18:07: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 06:18:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:18:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:18:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:18:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:18:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3426796/SRX3426796.20_summits.bed INFO @ Sat, 03 Apr 2021 06:18:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1686 records, 4 fields): 5 millis CompletedMACS2peakCalling