Job ID = 12264889 SRX = SRX3032287 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12761329 spots for SRR5863977/SRR5863977.sra Written 12761329 spots for SRR5863977/SRR5863977.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265044 ("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: 00:03:05 12761329 reads; of these: 12761329 (100.00%) were unpaired; of these: 4688182 (36.74%) aligned 0 times 6740913 (52.82%) aligned exactly 1 time 1332234 (10.44%) aligned >1 times 63.26% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 2656170 / 8073147 = 0.3290 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 06:00:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.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 06:00:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:00:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:00:45: 1000000 INFO @ Sat, 03 Apr 2021 06:00:54: 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 06:01:03: 3000000 INFO @ Sat, 03 Apr 2021 06:01:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.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 06:01:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:13: 4000000 INFO @ Sat, 03 Apr 2021 06:01:17: 1000000 INFO @ Sat, 03 Apr 2021 06:01:22: 5000000 INFO @ Sat, 03 Apr 2021 06:01:26: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:01:26: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:01:26: #1 total tags in treatment: 5416977 INFO @ Sat, 03 Apr 2021 06:01:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:26: #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 06:01:26: #1 tags after filtering in treatment: 5416977 INFO @ Sat, 03 Apr 2021 06:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:27: 2000000 INFO @ Sat, 03 Apr 2021 06:01:27: #2 number of paired peaks: 4745 INFO @ Sat, 03 Apr 2021 06:01:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:27: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:27: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:27: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:27: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Apr 2021 06:01:27: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Apr 2021 06:01:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.05_model.r WARNING @ Sat, 03 Apr 2021 06:01:27: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:01:27: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Apr 2021 06:01:27: #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 06:01:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:27: #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 06:01:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.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 06:01:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:36: 3000000 INFO @ Sat, 03 Apr 2021 06:01:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:45: 1000000 INFO @ Sat, 03 Apr 2021 06:01:46: 4000000 INFO @ Sat, 03 Apr 2021 06:01:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.05_summits.bed INFO @ Sat, 03 Apr 2021 06:01:54: Done! INFO @ Sat, 03 Apr 2021 06:01:54: 2000000 pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (14444 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:01:56: 5000000 INFO @ Sat, 03 Apr 2021 06:02:01: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:02:01: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:02:01: #1 total tags in treatment: 5416977 INFO @ Sat, 03 Apr 2021 06:02:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:01: #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 06:02:01: #1 tags after filtering in treatment: 5416977 INFO @ Sat, 03 Apr 2021 06:02:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:01: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:02: #2 number of paired peaks: 4745 INFO @ Sat, 03 Apr 2021 06:02:02: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:02: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:02: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:02: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:02: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Apr 2021 06:02:02: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Apr 2021 06:02:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.10_model.r WARNING @ Sat, 03 Apr 2021 06:02:02: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:02: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Apr 2021 06:02:02: #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 06:02:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:04: 3000000 INFO @ Sat, 03 Apr 2021 06:02:13: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:02:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:22: 5000000 INFO @ Sat, 03 Apr 2021 06:02:26: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 06:02:26: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 06:02:26: #1 total tags in treatment: 5416977 INFO @ Sat, 03 Apr 2021 06:02:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:26: #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 06:02:26: #1 tags after filtering in treatment: 5416977 INFO @ Sat, 03 Apr 2021 06:02:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:27: #2 number of paired peaks: 4745 INFO @ Sat, 03 Apr 2021 06:02:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:27: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:27: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:27: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:27: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Apr 2021 06:02:27: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 03 Apr 2021 06:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.20_model.r WARNING @ Sat, 03 Apr 2021 06:02:27: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:27: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 03 Apr 2021 06:02:27: #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 06:02:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.10_summits.bed INFO @ Sat, 03 Apr 2021 06:02:28: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8450 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:02:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032287/SRX3032287.20_summits.bed INFO @ Sat, 03 Apr 2021 06:02:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2937 records, 4 fields): 9 millis CompletedMACS2peakCalling