Job ID = 14172198 SRX = SRX9427698 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15753714 spots for SRR12975505/SRR12975505.sra Written 15753714 spots for SRR12975505/SRR12975505.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172671 ("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: 00:04:05 15753714 reads; of these: 15753714 (100.00%) were unpaired; of these: 10319259 (65.50%) aligned 0 times 1691557 (10.74%) aligned exactly 1 time 3742898 (23.76%) aligned >1 times 34.50% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 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] 1517578 / 5434455 = 0.2793 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 14:52:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.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 14:52:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:52:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:52:39: 1000000 INFO @ Sat, 11 Dec 2021 14:52:45: 2000000 INFO @ Sat, 11 Dec 2021 14:52:50: 3000000 INFO @ Sat, 11 Dec 2021 14:52:55: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:52:55: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:52:55: #1 total tags in treatment: 3916877 INFO @ Sat, 11 Dec 2021 14:52:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:52:55: #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 14:52:55: #1 tags after filtering in treatment: 3916877 INFO @ Sat, 11 Dec 2021 14:52:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:52:55: #1 finished! INFO @ Sat, 11 Dec 2021 14:52:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:52:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:52:55: #2 number of paired peaks: 4346 INFO @ Sat, 11 Dec 2021 14:52:55: start model_add_line... INFO @ Sat, 11 Dec 2021 14:52:55: start X-correlation... INFO @ Sat, 11 Dec 2021 14:52:55: end of X-cor INFO @ Sat, 11 Dec 2021 14:52:55: #2 finished! INFO @ Sat, 11 Dec 2021 14:52:55: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 14:52:55: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 14:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.05_model.r WARNING @ Sat, 11 Dec 2021 14:52:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:52:56: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 14:52:56: #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 14:52:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:52:56: #3 Pre-compute pvalue-qvalue table... 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 14:53:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:53:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.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 14:53:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:53:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.05_summits.bed INFO @ Sat, 11 Dec 2021 14:53:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5416 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:53:09: 1000000 INFO @ Sat, 11 Dec 2021 14:53:15: 2000000 INFO @ Sat, 11 Dec 2021 14:53:20: 3000000 INFO @ Sat, 11 Dec 2021 14:53:25: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:53:25: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:53:25: #1 total tags in treatment: 3916877 INFO @ Sat, 11 Dec 2021 14:53:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:53:25: #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 14:53:25: #1 tags after filtering in treatment: 3916877 INFO @ Sat, 11 Dec 2021 14:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:53:25: #1 finished! INFO @ Sat, 11 Dec 2021 14:53:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:53:25: #2 number of paired peaks: 4346 INFO @ Sat, 11 Dec 2021 14:53:25: start model_add_line... INFO @ Sat, 11 Dec 2021 14:53:25: start X-correlation... INFO @ Sat, 11 Dec 2021 14:53:25: end of X-cor INFO @ Sat, 11 Dec 2021 14:53:25: #2 finished! INFO @ Sat, 11 Dec 2021 14:53:25: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 14:53:25: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 14:53:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.10_model.r WARNING @ Sat, 11 Dec 2021 14:53:25: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:53:25: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 14:53:25: #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 14:53:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:53:25: #3 Pre-compute pvalue-qvalue table... 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 14:53:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:53:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.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 14:53:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:53:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.10_summits.bed INFO @ Sat, 11 Dec 2021 14:53:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1667 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:53:39: 1000000 INFO @ Sat, 11 Dec 2021 14:53:44: 2000000 INFO @ Sat, 11 Dec 2021 14:53:49: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:53:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:53:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:53:53: #1 total tags in treatment: 3916877 INFO @ Sat, 11 Dec 2021 14:53:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:53:53: #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 14:53:53: #1 tags after filtering in treatment: 3916877 INFO @ Sat, 11 Dec 2021 14:53:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:53:53: #1 finished! INFO @ Sat, 11 Dec 2021 14:53:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:53:53: #2 number of paired peaks: 4346 INFO @ Sat, 11 Dec 2021 14:53:53: start model_add_line... INFO @ Sat, 11 Dec 2021 14:53:53: start X-correlation... INFO @ Sat, 11 Dec 2021 14:53:53: end of X-cor INFO @ Sat, 11 Dec 2021 14:53:53: #2 finished! INFO @ Sat, 11 Dec 2021 14:53:53: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 14:53:53: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 14:53:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.20_model.r WARNING @ Sat, 11 Dec 2021 14:53:53: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:53:53: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 14:53:53: #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 14:53:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:53:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:54:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:54:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:54:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:54:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427698/SRX9427698.20_summits.bed INFO @ Sat, 11 Dec 2021 14:54:06: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (656 records, 4 fields): 1 millis CompletedMACS2peakCalling