Job ID = 10165841 SRX = SRX7723689 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14707499 spots for SRR11084645/SRR11084645.sra Written 14707499 spots for SRR11084645/SRR11084645.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166148 ("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: 00:04:56 14707499 reads; of these: 14707499 (100.00%) were unpaired; of these: 3092829 (21.03%) aligned 0 times 9998205 (67.98%) aligned exactly 1 time 1616465 (10.99%) aligned >1 times 78.97% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2525577 / 11614670 = 0.2174 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.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 @ Thu, 08 Oct 2020 20:07:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:07:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:07:45: 1000000 INFO @ Thu, 08 Oct 2020 20:07:51: 2000000 INFO @ Thu, 08 Oct 2020 20:07:56: 3000000 INFO @ Thu, 08 Oct 2020 20:08:02: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:08:08: 5000000 INFO @ Thu, 08 Oct 2020 20:08:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.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 @ Thu, 08 Oct 2020 20:08:08: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:08:08: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:08:14: 6000000 INFO @ Thu, 08 Oct 2020 20:08:15: 1000000 INFO @ Thu, 08 Oct 2020 20:08:21: 7000000 INFO @ Thu, 08 Oct 2020 20:08:21: 2000000 INFO @ Thu, 08 Oct 2020 20:08:27: 8000000 INFO @ Thu, 08 Oct 2020 20:08:28: 3000000 INFO @ Thu, 08 Oct 2020 20:08:33: 9000000 INFO @ Thu, 08 Oct 2020 20:08:34: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:08:34: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:08:34: #1 total tags in treatment: 9089093 INFO @ Thu, 08 Oct 2020 20:08:34: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:08:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:08:34: #1 tags after filtering in treatment: 9089093 INFO @ Thu, 08 Oct 2020 20:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:08:34: #1 finished! INFO @ Thu, 08 Oct 2020 20:08:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:08:34: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:08:35: #2 number of paired peaks: 675 WARNING @ Thu, 08 Oct 2020 20:08:35: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Thu, 08 Oct 2020 20:08:35: start model_add_line... INFO @ Thu, 08 Oct 2020 20:08:35: start X-correlation... INFO @ Thu, 08 Oct 2020 20:08:35: end of X-cor INFO @ Thu, 08 Oct 2020 20:08:35: #2 finished! INFO @ Thu, 08 Oct 2020 20:08:35: #2 predicted fragment length is 112 bps INFO @ Thu, 08 Oct 2020 20:08:35: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 08 Oct 2020 20:08:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05_model.r WARNING @ Thu, 08 Oct 2020 20:08:35: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:08:35: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Thu, 08 Oct 2020 20:08:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:08:35: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:08:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.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 @ Thu, 08 Oct 2020 20:08:38: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:08:38: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:08:40: 5000000 INFO @ Thu, 08 Oct 2020 20:08:44: 1000000 INFO @ Thu, 08 Oct 2020 20:08:46: 6000000 INFO @ Thu, 08 Oct 2020 20:08:51: 2000000 INFO @ Thu, 08 Oct 2020 20:08:53: 7000000 INFO @ Thu, 08 Oct 2020 20:08:56: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:08:57: 3000000 INFO @ Thu, 08 Oct 2020 20:08:59: 8000000 INFO @ Thu, 08 Oct 2020 20:09:03: 4000000 INFO @ Thu, 08 Oct 2020 20:09:05: 9000000 INFO @ Thu, 08 Oct 2020 20:09:05: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:09:05: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:09:05: #1 total tags in treatment: 9089093 INFO @ Thu, 08 Oct 2020 20:09:05: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:09:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:09:06: #1 tags after filtering in treatment: 9089093 INFO @ Thu, 08 Oct 2020 20:09:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:09:06: #1 finished! INFO @ Thu, 08 Oct 2020 20:09:06: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:09:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:09:06: #2 number of paired peaks: 675 WARNING @ Thu, 08 Oct 2020 20:09:06: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Thu, 08 Oct 2020 20:09:06: start model_add_line... INFO @ Thu, 08 Oct 2020 20:09:06: start X-correlation... INFO @ Thu, 08 Oct 2020 20:09:06: end of X-cor INFO @ Thu, 08 Oct 2020 20:09:06: #2 finished! INFO @ Thu, 08 Oct 2020 20:09:06: #2 predicted fragment length is 112 bps INFO @ Thu, 08 Oct 2020 20:09:06: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 08 Oct 2020 20:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10_model.r WARNING @ Thu, 08 Oct 2020 20:09:06: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:09:06: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Thu, 08 Oct 2020 20:09:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:09:06: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:09:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:09:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:09:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05_summits.bed INFO @ Thu, 08 Oct 2020 20:09:08: Done! INFO @ Thu, 08 Oct 2020 20:09:09: 5000000 pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (16903 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:09:15: 6000000 INFO @ Thu, 08 Oct 2020 20:09:21: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:09:26: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:09:27: 8000000 INFO @ Thu, 08 Oct 2020 20:09:32: 9000000 INFO @ Thu, 08 Oct 2020 20:09:33: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:09:33: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:09:33: #1 total tags in treatment: 9089093 INFO @ Thu, 08 Oct 2020 20:09:33: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:09:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:09:33: #1 tags after filtering in treatment: 9089093 INFO @ Thu, 08 Oct 2020 20:09:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:09:33: #1 finished! INFO @ Thu, 08 Oct 2020 20:09:33: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:09:34: #2 number of paired peaks: 675 WARNING @ Thu, 08 Oct 2020 20:09:34: Fewer paired peaks (675) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 675 pairs to build model! INFO @ Thu, 08 Oct 2020 20:09:34: start model_add_line... INFO @ Thu, 08 Oct 2020 20:09:34: start X-correlation... INFO @ Thu, 08 Oct 2020 20:09:34: end of X-cor INFO @ Thu, 08 Oct 2020 20:09:34: #2 finished! INFO @ Thu, 08 Oct 2020 20:09:34: #2 predicted fragment length is 112 bps INFO @ Thu, 08 Oct 2020 20:09:34: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 08 Oct 2020 20:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20_model.r WARNING @ Thu, 08 Oct 2020 20:09:34: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:09:34: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Thu, 08 Oct 2020 20:09:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:09:34: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:09:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10_summits.bed INFO @ Thu, 08 Oct 2020 20:09:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7373 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:09:55: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:10:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:10:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:10:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20_summits.bed INFO @ Thu, 08 Oct 2020 20:10:06: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1822 records, 4 fields): 3 millis CompletedMACS2peakCalling