Job ID = 14167070 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 14167465 ("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: 00:05:52 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: 00:05:52 Overall time: 00:05:52 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 09:40:45: # 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 @ Fri, 10 Dec 2021 09:40:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:40:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:40:53: 1000000 INFO @ Fri, 10 Dec 2021 09:41:01: 2000000 INFO @ Fri, 10 Dec 2021 09:41:09: 3000000 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 @ Fri, 10 Dec 2021 09:41:15: # 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 @ Fri, 10 Dec 2021 09:41:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:41:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:41:16: 4000000 INFO @ Fri, 10 Dec 2021 09:41:23: 1000000 INFO @ Fri, 10 Dec 2021 09:41:25: 5000000 INFO @ Fri, 10 Dec 2021 09:41:32: 2000000 INFO @ Fri, 10 Dec 2021 09:41:33: 6000000 INFO @ Fri, 10 Dec 2021 09:41:39: 3000000 INFO @ Fri, 10 Dec 2021 09:41:42: 7000000 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 @ Fri, 10 Dec 2021 09:41:45: # 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 @ Fri, 10 Dec 2021 09:41:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:41:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:41:47: 4000000 INFO @ Fri, 10 Dec 2021 09:41:50: 8000000 INFO @ Fri, 10 Dec 2021 09:41:51: 1000000 INFO @ Fri, 10 Dec 2021 09:41:55: 5000000 INFO @ Fri, 10 Dec 2021 09:41:57: 2000000 INFO @ Fri, 10 Dec 2021 09:41:58: 9000000 INFO @ Fri, 10 Dec 2021 09:41:59: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:41:59: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:41:59: #1 total tags in treatment: 9089093 INFO @ Fri, 10 Dec 2021 09:41:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:41:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:41:59: #1 tags after filtering in treatment: 9089093 INFO @ Fri, 10 Dec 2021 09:41:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:41:59: #1 finished! INFO @ Fri, 10 Dec 2021 09:41:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:42:00: #2 number of paired peaks: 675 WARNING @ Fri, 10 Dec 2021 09:42:00: 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 @ Fri, 10 Dec 2021 09:42:00: start model_add_line... INFO @ Fri, 10 Dec 2021 09:42:00: start X-correlation... INFO @ Fri, 10 Dec 2021 09:42:00: end of X-cor INFO @ Fri, 10 Dec 2021 09:42:00: #2 finished! INFO @ Fri, 10 Dec 2021 09:42:00: #2 predicted fragment length is 112 bps INFO @ Fri, 10 Dec 2021 09:42:00: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 10 Dec 2021 09:42:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05_model.r WARNING @ Fri, 10 Dec 2021 09:42:00: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:42:00: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Fri, 10 Dec 2021 09:42:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:42:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:42:03: 6000000 INFO @ Fri, 10 Dec 2021 09:42:03: 3000000 INFO @ Fri, 10 Dec 2021 09:42:09: 4000000 INFO @ Fri, 10 Dec 2021 09:42:10: 7000000 INFO @ Fri, 10 Dec 2021 09:42:16: 5000000 INFO @ Fri, 10 Dec 2021 09:42:17: 8000000 INFO @ Fri, 10 Dec 2021 09:42:22: 6000000 INFO @ Fri, 10 Dec 2021 09:42:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:42:25: 9000000 INFO @ Fri, 10 Dec 2021 09:42:26: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:42:26: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:42:26: #1 total tags in treatment: 9089093 INFO @ Fri, 10 Dec 2021 09:42:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:42:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:42:26: #1 tags after filtering in treatment: 9089093 INFO @ Fri, 10 Dec 2021 09:42:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:42:26: #1 finished! INFO @ Fri, 10 Dec 2021 09:42:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:42:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:42:27: #2 number of paired peaks: 675 WARNING @ Fri, 10 Dec 2021 09:42:27: 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 @ Fri, 10 Dec 2021 09:42:27: start model_add_line... INFO @ Fri, 10 Dec 2021 09:42:27: start X-correlation... INFO @ Fri, 10 Dec 2021 09:42:27: end of X-cor INFO @ Fri, 10 Dec 2021 09:42:27: #2 finished! INFO @ Fri, 10 Dec 2021 09:42:27: #2 predicted fragment length is 112 bps INFO @ Fri, 10 Dec 2021 09:42:27: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 10 Dec 2021 09:42:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10_model.r WARNING @ Fri, 10 Dec 2021 09:42:27: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:42:27: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Fri, 10 Dec 2021 09:42:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:42:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:42:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:42:28: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:42:33: 8000000 INFO @ Fri, 10 Dec 2021 09:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.05_summits.bed INFO @ Fri, 10 Dec 2021 09:42:35: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (16903 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:42:39: 9000000 INFO @ Fri, 10 Dec 2021 09:42:39: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:42:39: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:42:39: #1 total tags in treatment: 9089093 INFO @ Fri, 10 Dec 2021 09:42:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:42:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 09:42:39: #1 tags after filtering in treatment: 9089093 INFO @ Fri, 10 Dec 2021 09:42:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:42:39: #1 finished! INFO @ Fri, 10 Dec 2021 09:42:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:42:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:42:40: #2 number of paired peaks: 675 WARNING @ Fri, 10 Dec 2021 09:42:40: 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 @ Fri, 10 Dec 2021 09:42:40: start model_add_line... INFO @ Fri, 10 Dec 2021 09:42:40: start X-correlation... INFO @ Fri, 10 Dec 2021 09:42:40: end of X-cor INFO @ Fri, 10 Dec 2021 09:42:40: #2 finished! INFO @ Fri, 10 Dec 2021 09:42:40: #2 predicted fragment length is 112 bps INFO @ Fri, 10 Dec 2021 09:42:40: #2 alternative fragment length(s) may be 112 bps INFO @ Fri, 10 Dec 2021 09:42:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20_model.r WARNING @ Fri, 10 Dec 2021 09:42:40: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:42:40: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Fri, 10 Dec 2021 09:42:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 09:42:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:42:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 09:42:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.10_summits.bed INFO @ Fri, 10 Dec 2021 09:43:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7373 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:43:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:43:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:43:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723689/SRX7723689.20_summits.bed INFO @ Fri, 10 Dec 2021 09:43:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1822 records, 4 fields): 4 millis CompletedMACS2peakCalling