Job ID = 12264895 SRX = SRX3032293 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12324622 spots for SRR5863983/SRR5863983.sra Written 12324622 spots for SRR5863983/SRR5863983.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265060 ("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: 00:03:54 12324622 reads; of these: 12324622 (100.00%) were unpaired; of these: 5324608 (43.20%) aligned 0 times 5711101 (46.34%) aligned exactly 1 time 1288913 (10.46%) aligned >1 times 56.80% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 2249685 / 7000014 = 0.3214 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 06:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.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 06:01:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:02: 1000000 INFO @ Sat, 03 Apr 2021 06:02:10: 2000000 INFO @ Sat, 03 Apr 2021 06:02:17: 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 06:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.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 06:02:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:25: 4000000 INFO @ Sat, 03 Apr 2021 06:02:32: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:02:32: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:02:32: #1 total tags in treatment: 4750329 INFO @ Sat, 03 Apr 2021 06:02:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:32: #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 06:02:32: #1 tags after filtering in treatment: 4750329 INFO @ Sat, 03 Apr 2021 06:02:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:32: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:33: 1000000 INFO @ Sat, 03 Apr 2021 06:02:33: #2 number of paired peaks: 5821 INFO @ Sat, 03 Apr 2021 06:02:33: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:33: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:33: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:33: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:33: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 06:02:33: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 06:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.05_model.r WARNING @ Sat, 03 Apr 2021 06:02:33: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:33: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 06:02:33: #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 06:02:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:02:40: 2000000 INFO @ Sat, 03 Apr 2021 06:02:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:47: 3000000 INFO @ Sat, 03 Apr 2021 06:02:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.05_summits.bed INFO @ Sat, 03 Apr 2021 06:02:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11691 records, 4 fields): 18 millis CompletedMACS2peakCalling 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 06:02:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.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 06:02:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:54: 4000000 INFO @ Sat, 03 Apr 2021 06:03:00: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:03:00: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:03:00: #1 total tags in treatment: 4750329 INFO @ Sat, 03 Apr 2021 06:03:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:00: #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 06:03:00: #1 tags after filtering in treatment: 4750329 INFO @ Sat, 03 Apr 2021 06:03:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:00: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:00: #2 number of paired peaks: 5821 INFO @ Sat, 03 Apr 2021 06:03:00: start model_add_line... INFO @ Sat, 03 Apr 2021 06:03:00: start X-correlation... INFO @ Sat, 03 Apr 2021 06:03:00: end of X-cor INFO @ Sat, 03 Apr 2021 06:03:00: #2 finished! INFO @ Sat, 03 Apr 2021 06:03:00: #2 predicted fragment length is 98 bps INFO @ Sat, 03 Apr 2021 06:03:00: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 06:03:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.10_model.r WARNING @ Sat, 03 Apr 2021 06:03:00: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:03:00: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Sat, 03 Apr 2021 06:03:00: #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 06:03:00: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:03:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:03:01: 1000000 INFO @ Sat, 03 Apr 2021 06:03:09: 2000000 INFO @ Sat, 03 Apr 2021 06:03:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:16: 3000000 INFO @ Sat, 03 Apr 2021 06:03:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.10_summits.bed INFO @ Sat, 03 Apr 2021 06:03:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7774 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:03:23: 4000000 INFO @ Sat, 03 Apr 2021 06:03:28: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:03:28: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:03:28: #1 total tags in treatment: 4750329 INFO @ Sat, 03 Apr 2021 06:03:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:03:28: #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 06:03:28: #1 tags after filtering in treatment: 4750329 INFO @ Sat, 03 Apr 2021 06:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:03:28: #1 finished! INFO @ Sat, 03 Apr 2021 06:03:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:03:28: #2 number of paired peaks: 5821 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 98 bps INFO @ Sat, 03 Apr 2021 06:03:28: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 03 Apr 2021 06:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.20_model.r WARNING @ Sat, 03 Apr 2021 06:03:28: #2 Since the d (98) 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): 98 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... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:03:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032293/SRX3032293.20_summits.bed INFO @ Sat, 03 Apr 2021 06:03:45: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3641 records, 4 fields): 21 millis CompletedMACS2peakCalling