Job ID = 12264882 SRX = SRX3032280 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14146139 spots for SRR5863970/SRR5863970.sra Written 14146139 spots for SRR5863970/SRR5863970.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265048 ("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: 00:03:39 14146139 reads; of these: 14146139 (100.00%) were unpaired; of these: 2328629 (16.46%) aligned 0 times 9074313 (64.15%) aligned exactly 1 time 2743197 (19.39%) aligned >1 times 83.54% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4597966 / 11817510 = 0.3891 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 06:01:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.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 06:01:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:52: 1000000 INFO @ Sat, 03 Apr 2021 06:01:59: 2000000 INFO @ Sat, 03 Apr 2021 06:02:06: 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 06:02:14: 4000000 INFO @ Sat, 03 Apr 2021 06:02:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.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 06:02:14: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:14: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:21: 5000000 INFO @ Sat, 03 Apr 2021 06:02:25: 1000000 INFO @ Sat, 03 Apr 2021 06:02:28: 6000000 INFO @ Sat, 03 Apr 2021 06:02:34: 2000000 INFO @ Sat, 03 Apr 2021 06:02:36: 7000000 INFO @ Sat, 03 Apr 2021 06:02:37: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:02:37: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:02:37: #1 total tags in treatment: 7219544 INFO @ Sat, 03 Apr 2021 06:02:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:37: #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 06:02:38: #1 tags after filtering in treatment: 7219544 INFO @ Sat, 03 Apr 2021 06:02:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:38: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:39: #2 number of paired peaks: 2868 INFO @ Sat, 03 Apr 2021 06:02:39: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:39: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:39: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:39: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:39: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 06:02:39: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Apr 2021 06:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.05_model.r WARNING @ Sat, 03 Apr 2021 06:02:39: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:39: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Apr 2021 06:02:39: #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 06:02:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:39: #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 06:02:44: 3000000 INFO @ Sat, 03 Apr 2021 06:02:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.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 06:02:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:53: 1000000 INFO @ Sat, 03 Apr 2021 06:02:55: 4000000 INFO @ Sat, 03 Apr 2021 06:03:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:02: 2000000 INFO @ Sat, 03 Apr 2021 06:03:05: 5000000 INFO @ Sat, 03 Apr 2021 06:03:10: 3000000 INFO @ Sat, 03 Apr 2021 06:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.05_summits.bed INFO @ Sat, 03 Apr 2021 06:03:14: Done! pass1 - making usageList (14 chroms): 7 millis pass2 - checking and writing primary data (17399 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:03:15: 6000000 INFO @ Sat, 03 Apr 2021 06:03:20: 4000000 INFO @ Sat, 03 Apr 2021 06:03:25: 7000000 INFO @ Sat, 03 Apr 2021 06:03:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:03:27: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:03:27: #1 total tags in treatment: 7219544 INFO @ Sat, 03 Apr 2021 06:03:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:27: #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 06:03:27: #1 tags after filtering in treatment: 7219544 INFO @ Sat, 03 Apr 2021 06:03:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:27: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:28: #2 number of paired peaks: 2868 INFO @ Sat, 03 Apr 2021 06:03:28: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:28: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:28: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:28: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:28: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 06:03:28: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Apr 2021 06:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.10_model.r WARNING @ Sat, 03 Apr 2021 06:03:28: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:03:28: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Apr 2021 06:03:28: #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 06:03:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:28: 5000000 INFO @ Sat, 03 Apr 2021 06:03:37: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:03:45: 7000000 INFO @ Sat, 03 Apr 2021 06:03:47: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:03:47: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:03:47: #1 total tags in treatment: 7219544 INFO @ Sat, 03 Apr 2021 06:03:47: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:47: #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 06:03:47: #1 tags after filtering in treatment: 7219544 INFO @ Sat, 03 Apr 2021 06:03:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:47: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:47: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:48: #2 number of paired peaks: 2868 INFO @ Sat, 03 Apr 2021 06:03:48: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:48: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:48: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:48: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:48: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 06:03:48: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 03 Apr 2021 06:03:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.20_model.r WARNING @ Sat, 03 Apr 2021 06:03:48: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:03:48: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 03 Apr 2021 06:03:48: #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 06:03:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.10_summits.bed INFO @ Sat, 03 Apr 2021 06:04:02: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9730 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:04:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032280/SRX3032280.20_summits.bed INFO @ Sat, 03 Apr 2021 06:04:22: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3220 records, 4 fields): 34 millis CompletedMACS2peakCalling