Job ID = 12264874 SRX = SRX3032273 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13589383 spots for SRR5863963/SRR5863963.sra Written 13589383 spots for SRR5863963/SRR5863963.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265072 ("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: 00:05:19 13589383 reads; of these: 13589383 (100.00%) were unpaired; of these: 5166716 (38.02%) aligned 0 times 7271879 (53.51%) aligned exactly 1 time 1150788 (8.47%) aligned >1 times 61.98% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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] 2916572 / 8422667 = 0.3463 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.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, 03 Apr 2021 06:03:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:03:35: 1000000 INFO @ Sat, 03 Apr 2021 06:03:44: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:03:54: 3000000 INFO @ Sat, 03 Apr 2021 06:03:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.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, 03 Apr 2021 06:03:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:03:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:03: 4000000 INFO @ Sat, 03 Apr 2021 06:04:05: 1000000 INFO @ Sat, 03 Apr 2021 06:04:12: 5000000 INFO @ Sat, 03 Apr 2021 06:04:15: 2000000 INFO @ Sat, 03 Apr 2021 06:04:17: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:04:17: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:04:17: #1 total tags in treatment: 5506095 INFO @ Sat, 03 Apr 2021 06:04:17: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:04:17: #1 tags after filtering in treatment: 5506095 INFO @ Sat, 03 Apr 2021 06:04:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:17: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:17: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:18: #2 number of paired peaks: 4767 INFO @ Sat, 03 Apr 2021 06:04:18: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:18: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:18: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:18: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:18: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:04:18: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.05_model.r WARNING @ Sat, 03 Apr 2021 06:04:18: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:18: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 06:04:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:04:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:04:24: 3000000 INFO @ Sat, 03 Apr 2021 06:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.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, 03 Apr 2021 06:04:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:04:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:04:34: 4000000 INFO @ Sat, 03 Apr 2021 06:04:34: 1000000 INFO @ Sat, 03 Apr 2021 06:04:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:04:42: 2000000 INFO @ Sat, 03 Apr 2021 06:04:43: 5000000 INFO @ Sat, 03 Apr 2021 06:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.05_summits.bed INFO @ Sat, 03 Apr 2021 06:04:45: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (14239 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:04:48: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:04:48: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:04:48: #1 total tags in treatment: 5506095 INFO @ Sat, 03 Apr 2021 06:04:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:04:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:04:48: #1 tags after filtering in treatment: 5506095 INFO @ Sat, 03 Apr 2021 06:04:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:04:48: #1 finished! INFO @ Sat, 03 Apr 2021 06:04:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:04:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:04:49: #2 number of paired peaks: 4767 INFO @ Sat, 03 Apr 2021 06:04:49: start model_add_line... INFO @ Sat, 03 Apr 2021 06:04:49: start X-correlation... INFO @ Sat, 03 Apr 2021 06:04:49: end of X-cor INFO @ Sat, 03 Apr 2021 06:04:49: #2 finished! INFO @ Sat, 03 Apr 2021 06:04:49: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:04:49: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:04:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.10_model.r WARNING @ Sat, 03 Apr 2021 06:04:49: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:04:49: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 06:04:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:04:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:04:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:04:50: 3000000 INFO @ Sat, 03 Apr 2021 06:04:58: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:05:06: 5000000 INFO @ Sat, 03 Apr 2021 06:05:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:05:09: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:05:09: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:05:09: #1 total tags in treatment: 5506095 INFO @ Sat, 03 Apr 2021 06:05:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:05:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:05:10: #1 tags after filtering in treatment: 5506095 INFO @ Sat, 03 Apr 2021 06:05:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:05:10: #1 finished! INFO @ Sat, 03 Apr 2021 06:05:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:05:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:05:10: #2 number of paired peaks: 4767 INFO @ Sat, 03 Apr 2021 06:05:10: start model_add_line... INFO @ Sat, 03 Apr 2021 06:05:11: start X-correlation... INFO @ Sat, 03 Apr 2021 06:05:11: end of X-cor INFO @ Sat, 03 Apr 2021 06:05:11: #2 finished! INFO @ Sat, 03 Apr 2021 06:05:11: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 06:05:11: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 06:05:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.20_model.r WARNING @ Sat, 03 Apr 2021 06:05:11: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:05:11: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 06:05:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:05:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:05:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:05:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:05:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:05:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.10_summits.bed INFO @ Sat, 03 Apr 2021 06:05:15: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9077 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:05:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:05:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:05:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032273/SRX3032273.20_summits.bed INFO @ Sat, 03 Apr 2021 06:05:36: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3791 records, 4 fields): 8 millis CompletedMACS2peakCalling