Job ID = 14170396 SRX = SRX8689017 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6964666 spots for SRR12174273/SRR12174273.sra Written 6964666 spots for SRR12174273/SRR12174273.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170802 ("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: 00:02:40 6964666 reads; of these: 6964666 (100.00%) were unpaired; of these: 385616 (5.54%) aligned 0 times 4685967 (67.28%) aligned exactly 1 time 1893083 (27.18%) aligned >1 times 94.46% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 335335 / 6579050 = 0.0510 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 @ Sat, 11 Dec 2021 06:46:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.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, 11 Dec 2021 06:46:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:46:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:46:54: 1000000 INFO @ Sat, 11 Dec 2021 06:46:59: 2000000 INFO @ Sat, 11 Dec 2021 06:47:05: 3000000 INFO @ Sat, 11 Dec 2021 06:47:11: 4000000 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 @ Sat, 11 Dec 2021 06:47:17: 5000000 INFO @ Sat, 11 Dec 2021 06:47:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.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, 11 Dec 2021 06:47:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:23: 6000000 INFO @ Sat, 11 Dec 2021 06:47:24: 1000000 INFO @ Sat, 11 Dec 2021 06:47:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:24: #1 total tags in treatment: 6243715 INFO @ Sat, 11 Dec 2021 06:47:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:47:24: #1 tags after filtering in treatment: 6243715 INFO @ Sat, 11 Dec 2021 06:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:24: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:25: #2 number of paired peaks: 431 WARNING @ Sat, 11 Dec 2021 06:47:25: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:25: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:25: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:25: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:25: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:25: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:47:25: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 06:47:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.05_model.r WARNING @ Sat, 11 Dec 2021 06:47:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:25: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 06:47:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:47:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:30: 2000000 INFO @ Sat, 11 Dec 2021 06:47:36: 3000000 INFO @ Sat, 11 Dec 2021 06:47:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:47:41: 4000000 INFO @ Sat, 11 Dec 2021 06:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.05_summits.bed INFO @ Sat, 11 Dec 2021 06:47:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1663 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 @ Sat, 11 Dec 2021 06:47:47: 5000000 INFO @ Sat, 11 Dec 2021 06:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.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, 11 Dec 2021 06:47:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:53: 6000000 INFO @ Sat, 11 Dec 2021 06:47:55: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:55: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:55: #1 total tags in treatment: 6243715 INFO @ Sat, 11 Dec 2021 06:47:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:47:55: #1 tags after filtering in treatment: 6243715 INFO @ Sat, 11 Dec 2021 06:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:55: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:55: #2 number of paired peaks: 431 WARNING @ Sat, 11 Dec 2021 06:47:55: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:55: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:55: 1000000 INFO @ Sat, 11 Dec 2021 06:47:55: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:55: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:55: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:55: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:47:55: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 06:47:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.10_model.r WARNING @ Sat, 11 Dec 2021 06:47:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:55: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 06:47:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:47:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:48:01: 2000000 INFO @ Sat, 11 Dec 2021 06:48:06: 3000000 INFO @ Sat, 11 Dec 2021 06:48:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:12: 4000000 INFO @ Sat, 11 Dec 2021 06:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.10_summits.bed INFO @ Sat, 11 Dec 2021 06:48:14: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1188 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:18: 5000000 INFO @ Sat, 11 Dec 2021 06:48:23: 6000000 INFO @ Sat, 11 Dec 2021 06:48:25: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:48:25: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:48:25: #1 total tags in treatment: 6243715 INFO @ Sat, 11 Dec 2021 06:48:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:48:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:48:25: #1 tags after filtering in treatment: 6243715 INFO @ Sat, 11 Dec 2021 06:48:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:48:25: #1 finished! INFO @ Sat, 11 Dec 2021 06:48:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:48:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:48:25: #2 number of paired peaks: 431 WARNING @ Sat, 11 Dec 2021 06:48:25: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sat, 11 Dec 2021 06:48:25: start model_add_line... INFO @ Sat, 11 Dec 2021 06:48:26: start X-correlation... INFO @ Sat, 11 Dec 2021 06:48:26: end of X-cor INFO @ Sat, 11 Dec 2021 06:48:26: #2 finished! INFO @ Sat, 11 Dec 2021 06:48:26: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 06:48:26: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 06:48:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.20_model.r WARNING @ Sat, 11 Dec 2021 06:48:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:48:26: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 06:48:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:48:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:48:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:48:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689017/SRX8689017.20_summits.bed INFO @ Sat, 11 Dec 2021 06:48:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (851 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。