Job ID = 14171466 SRX = SRX9137157 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4993741 spots for SRR12655987/SRR12655987.sra Written 4993741 spots for SRR12655987/SRR12655987.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171950 ("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: 00:04:04 4993741 reads; of these: 4993741 (100.00%) were unpaired; of these: 869731 (17.42%) aligned 0 times 3231523 (64.71%) aligned exactly 1 time 892487 (17.87%) aligned >1 times 82.58% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 373660 / 4124010 = 0.0906 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 @ Sat, 11 Dec 2021 11:51:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.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, 11 Dec 2021 11:51:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:51:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:51:34: 1000000 INFO @ Sat, 11 Dec 2021 11:51:43: 2000000 INFO @ Sat, 11 Dec 2021 11:51:52: 3000000 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 @ Sat, 11 Dec 2021 11:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.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, 11 Dec 2021 11:51:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:51:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:51:59: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:51:59: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:51:59: #1 total tags in treatment: 3750350 INFO @ Sat, 11 Dec 2021 11:51:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:51:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:51:59: #1 tags after filtering in treatment: 3750350 INFO @ Sat, 11 Dec 2021 11:51:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:51:59: #1 finished! INFO @ Sat, 11 Dec 2021 11:51:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:00: #2 number of paired peaks: 9480 INFO @ Sat, 11 Dec 2021 11:52:00: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:00: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:00: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:00: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:00: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 11:52:00: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 11:52:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.05_model.r WARNING @ Sat, 11 Dec 2021 11:52:00: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:00: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Sat, 11 Dec 2021 11:52:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:52:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:03: 1000000 INFO @ Sat, 11 Dec 2021 11:52:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:52:11: 2000000 INFO @ Sat, 11 Dec 2021 11:52:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:52:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:52:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.05_summits.bed INFO @ Sat, 11 Dec 2021 11:52:13: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7020 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:52:18: 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 @ Sat, 11 Dec 2021 11:52:24: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:52:24: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:52:24: #1 total tags in treatment: 3750350 INFO @ Sat, 11 Dec 2021 11:52:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:52:24: #1 tags after filtering in treatment: 3750350 INFO @ Sat, 11 Dec 2021 11:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:52:24: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:25: #2 number of paired peaks: 9480 INFO @ Sat, 11 Dec 2021 11:52:25: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:25: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:25: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:25: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:25: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 11:52:25: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 11:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.10_model.r WARNING @ Sat, 11 Dec 2021 11:52:25: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:25: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Sat, 11 Dec 2021 11:52:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:52:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.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, 11 Dec 2021 11:52:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:52:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:52:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:52:34: 1000000 INFO @ Sat, 11 Dec 2021 11:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.10_summits.bed INFO @ Sat, 11 Dec 2021 11:52:38: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6399 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:52:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:52:52: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:52:58: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 11:52:58: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 11:52:58: #1 total tags in treatment: 3750350 INFO @ Sat, 11 Dec 2021 11:52:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:52:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 11:52:58: #1 tags after filtering in treatment: 3750350 INFO @ Sat, 11 Dec 2021 11:52:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:52:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:52:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:52:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:52:59: #2 number of paired peaks: 9480 INFO @ Sat, 11 Dec 2021 11:52:59: start model_add_line... INFO @ Sat, 11 Dec 2021 11:52:59: start X-correlation... INFO @ Sat, 11 Dec 2021 11:52:59: end of X-cor INFO @ Sat, 11 Dec 2021 11:52:59: #2 finished! INFO @ Sat, 11 Dec 2021 11:52:59: #2 predicted fragment length is 178 bps INFO @ Sat, 11 Dec 2021 11:52:59: #2 alternative fragment length(s) may be 178 bps INFO @ Sat, 11 Dec 2021 11:52:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.20_model.r WARNING @ Sat, 11 Dec 2021 11:52:59: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:52:59: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Sat, 11 Dec 2021 11:52:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 11:52:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:52:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:53:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:53:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:53:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9137157/SRX9137157.20_summits.bed INFO @ Sat, 11 Dec 2021 11:53:13: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5110 records, 4 fields): 7 millis CompletedMACS2peakCalling