Job ID = 12264861 SRX = SRX3032260 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6317083 spots for SRR5863950/SRR5863950.sra Written 6317083 spots for SRR5863950/SRR5863950.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265019 ("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: 00:02:46 6317083 reads; of these: 6317083 (100.00%) were unpaired; of these: 1762455 (27.90%) aligned 0 times 3964850 (62.76%) aligned exactly 1 time 589778 (9.34%) aligned >1 times 72.10% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 1364753 / 4554628 = 0.2996 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 05:59:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.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 05:59:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:59:11: 1000000 INFO @ Sat, 03 Apr 2021 05:59:21: 2000000 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 05:59:30: 3000000 INFO @ Sat, 03 Apr 2021 05:59:32: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 05:59:32: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 05:59:32: #1 total tags in treatment: 3189875 INFO @ Sat, 03 Apr 2021 05:59:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:59:32: #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 05:59:32: #1 tags after filtering in treatment: 3189875 INFO @ Sat, 03 Apr 2021 05:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:59:32: #1 finished! INFO @ Sat, 03 Apr 2021 05:59:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:59:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.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 05:59:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:59:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:59:33: #2 number of paired peaks: 6659 INFO @ Sat, 03 Apr 2021 05:59:33: start model_add_line... INFO @ Sat, 03 Apr 2021 05:59:33: start X-correlation... INFO @ Sat, 03 Apr 2021 05:59:33: end of X-cor INFO @ Sat, 03 Apr 2021 05:59:33: #2 finished! INFO @ Sat, 03 Apr 2021 05:59:33: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 05:59:33: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 03 Apr 2021 05:59:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.05_model.r WARNING @ Sat, 03 Apr 2021 05:59:33: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 05:59:33: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sat, 03 Apr 2021 05:59:33: #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 05:59:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:59:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 05:59:40: 1000000 INFO @ Sat, 03 Apr 2021 05:59:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 05:59:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.05_peaks.xls INFO @ Sat, 03 Apr 2021 05:59:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 05:59:48: 2000000 INFO @ Sat, 03 Apr 2021 05:59:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.05_summits.bed INFO @ Sat, 03 Apr 2021 05:59:49: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (13320 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 05:59:57: 3000000 INFO @ Sat, 03 Apr 2021 05:59:58: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 05:59:58: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 05:59:58: #1 total tags in treatment: 3189875 INFO @ Sat, 03 Apr 2021 05:59:58: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:59:58: #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 05:59:58: #1 tags after filtering in treatment: 3189875 INFO @ Sat, 03 Apr 2021 05:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:59:58: #1 finished! INFO @ Sat, 03 Apr 2021 05:59:58: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:59:59: #2 number of paired peaks: 6659 INFO @ Sat, 03 Apr 2021 05:59:59: start model_add_line... INFO @ Sat, 03 Apr 2021 05:59:59: start X-correlation... INFO @ Sat, 03 Apr 2021 05:59:59: end of X-cor INFO @ Sat, 03 Apr 2021 05:59:59: #2 finished! INFO @ Sat, 03 Apr 2021 05:59:59: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 05:59:59: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 03 Apr 2021 05:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.10_model.r WARNING @ Sat, 03 Apr 2021 05:59:59: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 05:59:59: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sat, 03 Apr 2021 05:59:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 05:59:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:59:59: #3 Pre-compute pvalue-qvalue table... 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 06:00:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.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 06:00:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:12: 1000000 INFO @ Sat, 03 Apr 2021 06:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.10_summits.bed INFO @ Sat, 03 Apr 2021 06:00:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8107 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:00:21: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:00:32: 3000000 INFO @ Sat, 03 Apr 2021 06:00:33: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:00:33: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:00:33: #1 total tags in treatment: 3189875 INFO @ Sat, 03 Apr 2021 06:00:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:00:33: #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 06:00:33: #1 tags after filtering in treatment: 3189875 INFO @ Sat, 03 Apr 2021 06:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:00:33: #1 finished! INFO @ Sat, 03 Apr 2021 06:00:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:00:33: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:00:34: #2 number of paired peaks: 6659 INFO @ Sat, 03 Apr 2021 06:00:34: start model_add_line... INFO @ Sat, 03 Apr 2021 06:00:34: start X-correlation... INFO @ Sat, 03 Apr 2021 06:00:34: end of X-cor INFO @ Sat, 03 Apr 2021 06:00:34: #2 finished! INFO @ Sat, 03 Apr 2021 06:00:34: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 06:00:34: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 03 Apr 2021 06:00:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.20_model.r WARNING @ Sat, 03 Apr 2021 06:00:34: #2 Since the d (107) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:00:34: #2 You may need to consider one of the other alternative d(s): 107 WARNING @ Sat, 03 Apr 2021 06:00:34: #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 06:00:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:00:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:00:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:00:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:00:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:00:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032260/SRX3032260.20_summits.bed INFO @ Sat, 03 Apr 2021 06:00:50: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3295 records, 4 fields): 15 millis CompletedMACS2peakCalling