Job ID = 16440078 SRX = SRX10987326 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31584503 spots for SRR14648801/SRR14648801.sra Written 31584503 spots for SRR14648801/SRR14648801.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440118 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:02 31584503 reads; of these: 31584503 (100.00%) were unpaired; of these: 29894741 (94.65%) aligned 0 times 1371383 (4.34%) aligned exactly 1 time 318379 (1.01%) aligned >1 times 5.35% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 207642 / 1689762 = 0.1229 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.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 @ Tue, 02 Aug 2022 17:10:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:10:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:10:58: 1000000 INFO @ Tue, 02 Aug 2022 17:11:02: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:11:02: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:11:02: #1 total tags in treatment: 1482120 INFO @ Tue, 02 Aug 2022 17:11:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:11:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:11:02: #1 tags after filtering in treatment: 1482120 INFO @ Tue, 02 Aug 2022 17:11:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:11:02: #1 finished! INFO @ Tue, 02 Aug 2022 17:11:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:11:02: #2 number of paired peaks: 1312 INFO @ Tue, 02 Aug 2022 17:11:02: start model_add_line... INFO @ Tue, 02 Aug 2022 17:11:02: start X-correlation... INFO @ Tue, 02 Aug 2022 17:11:02: end of X-cor INFO @ Tue, 02 Aug 2022 17:11:02: #2 finished! INFO @ Tue, 02 Aug 2022 17:11:02: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 17:11:02: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 17:11:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.05_model.r WARNING @ Tue, 02 Aug 2022 17:11:02: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:11:02: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 17:11:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:11:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:11:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.05_summits.bed INFO @ Tue, 02 Aug 2022 17:11:07: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (239 records, 4 fields): 23 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.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 @ Tue, 02 Aug 2022 17:11:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:11:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:11:27: 1000000 INFO @ Tue, 02 Aug 2022 17:11:31: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:11:31: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:11:31: #1 total tags in treatment: 1482120 INFO @ Tue, 02 Aug 2022 17:11:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:11:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:11:31: #1 tags after filtering in treatment: 1482120 INFO @ Tue, 02 Aug 2022 17:11:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:11:31: #1 finished! INFO @ Tue, 02 Aug 2022 17:11:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:11:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:11:31: #2 number of paired peaks: 1312 INFO @ Tue, 02 Aug 2022 17:11:31: start model_add_line... INFO @ Tue, 02 Aug 2022 17:11:31: start X-correlation... INFO @ Tue, 02 Aug 2022 17:11:31: end of X-cor INFO @ Tue, 02 Aug 2022 17:11:31: #2 finished! INFO @ Tue, 02 Aug 2022 17:11:31: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 17:11:31: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 17:11:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.10_model.r WARNING @ Tue, 02 Aug 2022 17:11:31: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:11:31: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 17:11:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:11:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:11:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:11:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.10_summits.bed INFO @ Tue, 02 Aug 2022 17:11:36: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:11:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.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 @ Tue, 02 Aug 2022 17:11:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:11:49: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:11:57: 1000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:12:01: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 17:12:01: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 17:12:01: #1 total tags in treatment: 1482120 INFO @ Tue, 02 Aug 2022 17:12:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:12:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:12:01: #1 tags after filtering in treatment: 1482120 INFO @ Tue, 02 Aug 2022 17:12:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:12:01: #1 finished! INFO @ Tue, 02 Aug 2022 17:12:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:12:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:12:01: #2 number of paired peaks: 1312 INFO @ Tue, 02 Aug 2022 17:12:01: start model_add_line... INFO @ Tue, 02 Aug 2022 17:12:01: start X-correlation... INFO @ Tue, 02 Aug 2022 17:12:01: end of X-cor INFO @ Tue, 02 Aug 2022 17:12:01: #2 finished! INFO @ Tue, 02 Aug 2022 17:12:01: #2 predicted fragment length is 88 bps INFO @ Tue, 02 Aug 2022 17:12:01: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 02 Aug 2022 17:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.20_model.r WARNING @ Tue, 02 Aug 2022 17:12:01: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:12:01: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 02 Aug 2022 17:12:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:12:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:12:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:12:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10987326/SRX10987326.20_summits.bed INFO @ Tue, 02 Aug 2022 17:12:07: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (60 records, 4 fields): 77 millis CompletedMACS2peakCalling