Job ID = 12264880 SRX = SRX3032279 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10911522 spots for SRR5863969/SRR5863969.sra Written 10911522 spots for SRR5863969/SRR5863969.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265062 ("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: 00:04:52 10911522 reads; of these: 10911522 (100.00%) were unpaired; of these: 4425540 (40.56%) aligned 0 times 5394073 (49.43%) aligned exactly 1 time 1091909 (10.01%) aligned >1 times 59.44% overall alignment rate Time searching: 00:04:52 Overall time: 00:04:52 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] 1829914 / 6485982 = 0.2821 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 06:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.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 06:02:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:30: 1000000 INFO @ Sat, 03 Apr 2021 06:02:42: 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 06:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.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 06:02:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:54: 3000000 INFO @ Sat, 03 Apr 2021 06:03:01: 1000000 INFO @ Sat, 03 Apr 2021 06:03:09: 4000000 INFO @ Sat, 03 Apr 2021 06:03:13: 2000000 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 06:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.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 06:03:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:18: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:03:18: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:03:18: #1 total tags in treatment: 4656068 INFO @ Sat, 03 Apr 2021 06:03:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:18: #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 06:03:19: #1 tags after filtering in treatment: 4656068 INFO @ Sat, 03 Apr 2021 06:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:19: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:19: #2 number of paired peaks: 4252 INFO @ Sat, 03 Apr 2021 06:03:19: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:19: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:19: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:19: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:19: #2 predicted fragment length is 104 bps INFO @ Sat, 03 Apr 2021 06:03:19: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 03 Apr 2021 06:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.05_model.r WARNING @ Sat, 03 Apr 2021 06:03:19: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:03:19: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sat, 03 Apr 2021 06:03:19: #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 06:03:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:26: 3000000 INFO @ Sat, 03 Apr 2021 06:03:33: 1000000 INFO @ Sat, 03 Apr 2021 06:03:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:41: 4000000 INFO @ Sat, 03 Apr 2021 06:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.05_summits.bed INFO @ Sat, 03 Apr 2021 06:03:43: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12040 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:03:47: 2000000 INFO @ Sat, 03 Apr 2021 06:03:50: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:03:50: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:03:50: #1 total tags in treatment: 4656068 INFO @ Sat, 03 Apr 2021 06:03:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:50: #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 06:03:50: #1 tags after filtering in treatment: 4656068 INFO @ Sat, 03 Apr 2021 06:03:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:50: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:51: #2 number of paired peaks: 4252 INFO @ Sat, 03 Apr 2021 06:03:51: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:51: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:51: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:51: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:51: #2 predicted fragment length is 104 bps INFO @ Sat, 03 Apr 2021 06:03:51: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 03 Apr 2021 06:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.10_model.r WARNING @ Sat, 03 Apr 2021 06:03:51: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:03:51: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sat, 03 Apr 2021 06:03:51: #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 06:03:51: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:03:59: 3000000 INFO @ Sat, 03 Apr 2021 06:04:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:12: 4000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.10_summits.bed INFO @ Sat, 03 Apr 2021 06:04:14: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7062 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:04:20: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:04:20: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:04:20: #1 total tags in treatment: 4656068 INFO @ Sat, 03 Apr 2021 06:04:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:20: #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 06:04:20: #1 tags after filtering in treatment: 4656068 INFO @ Sat, 03 Apr 2021 06:04:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:20: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:20: #2 number of paired peaks: 4252 INFO @ Sat, 03 Apr 2021 06:04:20: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:21: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:21: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:21: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:21: #2 predicted fragment length is 104 bps INFO @ Sat, 03 Apr 2021 06:04:21: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 03 Apr 2021 06:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.20_model.r WARNING @ Sat, 03 Apr 2021 06:04:21: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:21: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sat, 03 Apr 2021 06:04:21: #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 06:04:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032279/SRX3032279.20_summits.bed INFO @ Sat, 03 Apr 2021 06:04:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2639 records, 4 fields): 5 millis CompletedMACS2peakCalling