Job ID = 14170447 SRX = SRX8689025 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8301207 spots for SRR12174330/SRR12174330.sra Written 8301207 spots for SRR12174330/SRR12174330.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170854 ("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: 00:03:35 8301207 reads; of these: 8301207 (100.00%) were unpaired; of these: 382262 (4.60%) aligned 0 times 5360715 (64.58%) aligned exactly 1 time 2558230 (30.82%) aligned >1 times 95.40% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 459228 / 7918945 = 0.0580 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 06:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.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 06:54:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:54:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:54:48: 1000000 INFO @ Sat, 11 Dec 2021 06:54:55: 2000000 INFO @ Sat, 11 Dec 2021 06:55:03: 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 @ Sat, 11 Dec 2021 06:55:10: 4000000 INFO @ Sat, 11 Dec 2021 06:55:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.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 06:55:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:55:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:55:17: 5000000 INFO @ Sat, 11 Dec 2021 06:55:19: 1000000 INFO @ Sat, 11 Dec 2021 06:55:24: 6000000 INFO @ Sat, 11 Dec 2021 06:55:26: 2000000 INFO @ Sat, 11 Dec 2021 06:55:31: 7000000 INFO @ Sat, 11 Dec 2021 06:55:34: 3000000 INFO @ Sat, 11 Dec 2021 06:55:35: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:55:35: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:55:35: #1 total tags in treatment: 7459717 INFO @ Sat, 11 Dec 2021 06:55:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:55:35: #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 06:55:35: #1 tags after filtering in treatment: 7459717 INFO @ Sat, 11 Dec 2021 06:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:55:35: #1 finished! INFO @ Sat, 11 Dec 2021 06:55:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:55:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:55:35: #2 number of paired peaks: 310 WARNING @ Sat, 11 Dec 2021 06:55:35: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 11 Dec 2021 06:55:35: start model_add_line... INFO @ Sat, 11 Dec 2021 06:55:35: start X-correlation... INFO @ Sat, 11 Dec 2021 06:55:35: end of X-cor INFO @ Sat, 11 Dec 2021 06:55:35: #2 finished! INFO @ Sat, 11 Dec 2021 06:55:35: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 06:55:35: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 06:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.05_model.r WARNING @ Sat, 11 Dec 2021 06:55:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:55:35: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 06:55:35: #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 06:55:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:55:35: #3 Pre-compute pvalue-qvalue table... 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 06:55:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.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 06:55:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:55:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:55:41: 4000000 INFO @ Sat, 11 Dec 2021 06:55:49: 5000000 INFO @ Sat, 11 Dec 2021 06:55:49: 1000000 INFO @ Sat, 11 Dec 2021 06:55:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:55:56: 2000000 INFO @ Sat, 11 Dec 2021 06:55:56: 6000000 INFO @ Sat, 11 Dec 2021 06:55:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:55:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:55:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.05_summits.bed INFO @ Sat, 11 Dec 2021 06:55:58: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1529 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:56:03: 3000000 INFO @ Sat, 11 Dec 2021 06:56:04: 7000000 INFO @ Sat, 11 Dec 2021 06:56:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:56:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:56:07: #1 total tags in treatment: 7459717 INFO @ Sat, 11 Dec 2021 06:56:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:56:07: #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 06:56:07: #1 tags after filtering in treatment: 7459717 INFO @ Sat, 11 Dec 2021 06:56:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:56:07: #1 finished! INFO @ Sat, 11 Dec 2021 06:56:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:56:08: #2 number of paired peaks: 310 WARNING @ Sat, 11 Dec 2021 06:56:08: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 11 Dec 2021 06:56:08: start model_add_line... INFO @ Sat, 11 Dec 2021 06:56:08: start X-correlation... INFO @ Sat, 11 Dec 2021 06:56:08: end of X-cor INFO @ Sat, 11 Dec 2021 06:56:08: #2 finished! INFO @ Sat, 11 Dec 2021 06:56:08: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 06:56:08: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 06:56:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.10_model.r WARNING @ Sat, 11 Dec 2021 06:56:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:56:08: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 06:56:08: #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 06:56:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:56:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:56:10: 4000000 INFO @ Sat, 11 Dec 2021 06:56:17: 5000000 INFO @ Sat, 11 Dec 2021 06:56:22: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:56:23: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:56:30: 7000000 INFO @ Sat, 11 Dec 2021 06:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.10_summits.bed INFO @ Sat, 11 Dec 2021 06:56:30: Done! pass1 - making usageList (8 chroms): 6 millis pass2 - checking and writing primary data (1088 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:56:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:56:33: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:56:33: #1 total tags in treatment: 7459717 INFO @ Sat, 11 Dec 2021 06:56:33: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:56:33: #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 06:56:33: #1 tags after filtering in treatment: 7459717 INFO @ Sat, 11 Dec 2021 06:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:56:33: #1 finished! INFO @ Sat, 11 Dec 2021 06:56:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:56:34: #2 number of paired peaks: 310 WARNING @ Sat, 11 Dec 2021 06:56:34: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Sat, 11 Dec 2021 06:56:34: start model_add_line... INFO @ Sat, 11 Dec 2021 06:56:34: start X-correlation... INFO @ Sat, 11 Dec 2021 06:56:34: end of X-cor INFO @ Sat, 11 Dec 2021 06:56:34: #2 finished! INFO @ Sat, 11 Dec 2021 06:56:34: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 06:56:34: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 06:56:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.20_model.r WARNING @ Sat, 11 Dec 2021 06:56:34: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:56:34: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 06:56:34: #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 06:56:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:56:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:56:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689025/SRX8689025.20_summits.bed INFO @ Sat, 11 Dec 2021 06:56:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (818 records, 4 fields): 3 millis CompletedMACS2peakCalling