Job ID = 14171935 SRX = SRX9427701 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11877429 spots for SRR12975508/SRR12975508.sra Written 11877429 spots for SRR12975508/SRR12975508.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172397 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:44 11877429 reads; of these: 11877429 (100.00%) were unpaired; of these: 7507138 (63.21%) aligned 0 times 2108746 (17.75%) aligned exactly 1 time 2261545 (19.04%) aligned >1 times 36.79% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 1064595 / 4370291 = 0.2436 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 13:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.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 13:31:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:31:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:31:49: 1000000 INFO @ Sat, 11 Dec 2021 13:31:54: 2000000 INFO @ Sat, 11 Dec 2021 13:31:59: 3000000 INFO @ Sat, 11 Dec 2021 13:32:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:32:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:32:01: #1 total tags in treatment: 3305696 INFO @ Sat, 11 Dec 2021 13:32:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:32:01: #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 13:32:01: #1 tags after filtering in treatment: 3305696 INFO @ Sat, 11 Dec 2021 13:32:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:32:01: #1 finished! INFO @ Sat, 11 Dec 2021 13:32:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:32:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:32:01: #2 number of paired peaks: 1497 INFO @ Sat, 11 Dec 2021 13:32:01: start model_add_line... INFO @ Sat, 11 Dec 2021 13:32:01: start X-correlation... INFO @ Sat, 11 Dec 2021 13:32:01: end of X-cor INFO @ Sat, 11 Dec 2021 13:32:01: #2 finished! INFO @ Sat, 11 Dec 2021 13:32:01: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 13:32:01: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 13:32:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.05_model.r WARNING @ Sat, 11 Dec 2021 13:32:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:32:01: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 13:32:01: #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 13:32:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:32:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:32:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.05_summits.bed INFO @ Sat, 11 Dec 2021 13:32:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1848 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 13:32:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.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 13:32:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:32:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:32:19: 1000000 INFO @ Sat, 11 Dec 2021 13:32:24: 2000000 INFO @ Sat, 11 Dec 2021 13:32:29: 3000000 INFO @ Sat, 11 Dec 2021 13:32:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:32:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:32:30: #1 total tags in treatment: 3305696 INFO @ Sat, 11 Dec 2021 13:32:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:32:30: #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 13:32:31: #1 tags after filtering in treatment: 3305696 INFO @ Sat, 11 Dec 2021 13:32:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:32:31: #1 finished! INFO @ Sat, 11 Dec 2021 13:32:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:32:31: #2 number of paired peaks: 1497 INFO @ Sat, 11 Dec 2021 13:32:31: start model_add_line... INFO @ Sat, 11 Dec 2021 13:32:31: start X-correlation... INFO @ Sat, 11 Dec 2021 13:32:31: end of X-cor INFO @ Sat, 11 Dec 2021 13:32:31: #2 finished! INFO @ Sat, 11 Dec 2021 13:32:31: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 13:32:31: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 13:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.10_model.r WARNING @ Sat, 11 Dec 2021 13:32:31: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:32:31: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 13:32:31: #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 13:32:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:32:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:32:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:32:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:32:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.10_summits.bed INFO @ Sat, 11 Dec 2021 13:32:41: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (809 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 13:32:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.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 13:32:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:32:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:32:49: 1000000 INFO @ Sat, 11 Dec 2021 13:32:54: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:32:59: 3000000 INFO @ Sat, 11 Dec 2021 13:33:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:33:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:33:01: #1 total tags in treatment: 3305696 INFO @ Sat, 11 Dec 2021 13:33:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:33:01: #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 13:33:01: #1 tags after filtering in treatment: 3305696 INFO @ Sat, 11 Dec 2021 13:33:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:33:01: #1 finished! INFO @ Sat, 11 Dec 2021 13:33:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:33:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:33:01: #2 number of paired peaks: 1497 INFO @ Sat, 11 Dec 2021 13:33:01: start model_add_line... INFO @ Sat, 11 Dec 2021 13:33:01: start X-correlation... INFO @ Sat, 11 Dec 2021 13:33:01: end of X-cor INFO @ Sat, 11 Dec 2021 13:33:01: #2 finished! INFO @ Sat, 11 Dec 2021 13:33:01: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 13:33:01: #2 alternative fragment length(s) may be 51 bps INFO @ Sat, 11 Dec 2021 13:33:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.20_model.r WARNING @ Sat, 11 Dec 2021 13:33:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:33:01: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sat, 11 Dec 2021 13:33:01: #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 13:33:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:33:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:33:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427701/SRX9427701.20_summits.bed INFO @ Sat, 11 Dec 2021 13:33:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (348 records, 4 fields): 2 millis CompletedMACS2peakCalling