Job ID = 14171040 SRX = SRX10000682 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23478329 spots for SRR13606606/SRR13606606.sra Written 23478329 spots for SRR13606606/SRR13606606.sra Read 23267781 spots for SRR13606607/SRR13606607.sra Written 23267781 spots for SRR13606607/SRR13606607.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171514 ("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: 00:11:23 46746110 reads; of these: 46746110 (100.00%) were unpaired; of these: 44499415 (95.19%) aligned 0 times 1820545 (3.89%) aligned exactly 1 time 426150 (0.91%) aligned >1 times 4.81% overall alignment rate Time searching: 00:11:24 Overall time: 00:11:24 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] 273609 / 2246695 = 0.1218 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 09:30:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.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 09:30:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:30:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:31:13: 1000000 INFO @ Sat, 11 Dec 2021 09:31:26: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:31:26: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:31:26: #1 total tags in treatment: 1973086 INFO @ Sat, 11 Dec 2021 09:31:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:31:26: #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 09:31:26: #1 tags after filtering in treatment: 1973086 INFO @ Sat, 11 Dec 2021 09:31:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:31:26: #1 finished! INFO @ Sat, 11 Dec 2021 09:31:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:31:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:31:26: #2 number of paired peaks: 1443 INFO @ Sat, 11 Dec 2021 09:31:26: start model_add_line... INFO @ Sat, 11 Dec 2021 09:31:26: start X-correlation... INFO @ Sat, 11 Dec 2021 09:31:26: end of X-cor INFO @ Sat, 11 Dec 2021 09:31:26: #2 finished! INFO @ Sat, 11 Dec 2021 09:31:26: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 09:31:26: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 11 Dec 2021 09:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.05_model.r WARNING @ Sat, 11 Dec 2021 09:31:26: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:31:26: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 11 Dec 2021 09:31:26: #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 09:31:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:31:26: #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 09:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.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 09:31:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:31:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:31:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:31:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:31:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:31:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.05_summits.bed INFO @ Sat, 11 Dec 2021 09:31:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (701 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:31:42: 1000000 INFO @ Sat, 11 Dec 2021 09:31:54: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:31:54: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:31:54: #1 total tags in treatment: 1973086 INFO @ Sat, 11 Dec 2021 09:31:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:31:54: #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 09:31:54: #1 tags after filtering in treatment: 1973086 INFO @ Sat, 11 Dec 2021 09:31:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:31:54: #1 finished! INFO @ Sat, 11 Dec 2021 09:31:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:31:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:31:54: #2 number of paired peaks: 1443 INFO @ Sat, 11 Dec 2021 09:31:54: start model_add_line... INFO @ Sat, 11 Dec 2021 09:31:54: start X-correlation... INFO @ Sat, 11 Dec 2021 09:31:54: end of X-cor INFO @ Sat, 11 Dec 2021 09:31:54: #2 finished! INFO @ Sat, 11 Dec 2021 09:31:54: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 09:31:54: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 11 Dec 2021 09:31:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.10_model.r WARNING @ Sat, 11 Dec 2021 09:31:54: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:31:54: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 11 Dec 2021 09:31:54: #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 09:31:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:31:54: #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 09:31:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.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 09:31:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:31:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:32:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:32:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:32:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.10_summits.bed INFO @ Sat, 11 Dec 2021 09:32:01: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:32:12: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:32:25: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 09:32:25: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 09:32:25: #1 total tags in treatment: 1973086 INFO @ Sat, 11 Dec 2021 09:32:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:32:25: #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 09:32:25: #1 tags after filtering in treatment: 1973086 INFO @ Sat, 11 Dec 2021 09:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:32:25: #1 finished! INFO @ Sat, 11 Dec 2021 09:32:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:32:26: #2 number of paired peaks: 1443 INFO @ Sat, 11 Dec 2021 09:32:26: start model_add_line... INFO @ Sat, 11 Dec 2021 09:32:26: start X-correlation... INFO @ Sat, 11 Dec 2021 09:32:26: end of X-cor INFO @ Sat, 11 Dec 2021 09:32:26: #2 finished! INFO @ Sat, 11 Dec 2021 09:32:26: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 09:32:26: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 11 Dec 2021 09:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.20_model.r WARNING @ Sat, 11 Dec 2021 09:32:26: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:32:26: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 11 Dec 2021 09:32:26: #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 09:32:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:32:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:32:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:32:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:32:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000682/SRX10000682.20_summits.bed INFO @ Sat, 11 Dec 2021 09:32:32: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (86 records, 4 fields): 1 millis CompletedMACS2peakCalling