Job ID = 14167134 SRX = SRX4712950 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23488900 spots for SRR7874080/SRR7874080.sra Written 23488900 spots for SRR7874080/SRR7874080.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167596 ("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: 00:07:06 23488900 reads; of these: 23488900 (100.00%) were unpaired; of these: 2287335 (9.74%) aligned 0 times 16129362 (68.67%) aligned exactly 1 time 5072203 (21.59%) aligned >1 times 90.26% overall alignment rate Time searching: 00:07:06 Overall time: 00:07:06 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 12 files... [bam_rmdupse_core] 16689599 / 21201565 = 0.7872 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 10:31:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.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 10:31:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:31:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:32:02: 1000000 INFO @ Fri, 10 Dec 2021 10:32:07: 2000000 INFO @ Fri, 10 Dec 2021 10:32:12: 3000000 INFO @ Fri, 10 Dec 2021 10:32:16: 4000000 INFO @ Fri, 10 Dec 2021 10:32:19: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:32:19: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:32:19: #1 total tags in treatment: 4511966 INFO @ Fri, 10 Dec 2021 10:32:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:32:19: #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 10:32:19: #1 tags after filtering in treatment: 4511966 INFO @ Fri, 10 Dec 2021 10:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:32:19: #1 finished! INFO @ Fri, 10 Dec 2021 10:32:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:32:20: #2 number of paired peaks: 1839 INFO @ Fri, 10 Dec 2021 10:32:20: start model_add_line... INFO @ Fri, 10 Dec 2021 10:32:20: start X-correlation... INFO @ Fri, 10 Dec 2021 10:32:20: end of X-cor INFO @ Fri, 10 Dec 2021 10:32:20: #2 finished! INFO @ Fri, 10 Dec 2021 10:32:20: #2 predicted fragment length is 63 bps INFO @ Fri, 10 Dec 2021 10:32:20: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 10 Dec 2021 10:32:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.05_model.r WARNING @ Fri, 10 Dec 2021 10:32:20: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:32:20: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 10 Dec 2021 10:32:20: #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 10:32:20: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:32:20: #3 Pre-compute pvalue-qvalue table... 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 10:32:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.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 10:32:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:32:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:32:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:32:32: 1000000 INFO @ Fri, 10 Dec 2021 10:32:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:32:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:32:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.05_summits.bed INFO @ Fri, 10 Dec 2021 10:32:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4081 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:32:38: 2000000 INFO @ Fri, 10 Dec 2021 10:32:44: 3000000 INFO @ Fri, 10 Dec 2021 10:32:50: 4000000 INFO @ Fri, 10 Dec 2021 10:32:53: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:32:53: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:32:53: #1 total tags in treatment: 4511966 INFO @ Fri, 10 Dec 2021 10:32:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:32:53: #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 10:32:53: #1 tags after filtering in treatment: 4511966 INFO @ Fri, 10 Dec 2021 10:32:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:32:53: #1 finished! INFO @ Fri, 10 Dec 2021 10:32:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:32:54: #2 number of paired peaks: 1839 INFO @ Fri, 10 Dec 2021 10:32:54: start model_add_line... INFO @ Fri, 10 Dec 2021 10:32:54: start X-correlation... INFO @ Fri, 10 Dec 2021 10:32:54: end of X-cor INFO @ Fri, 10 Dec 2021 10:32:54: #2 finished! INFO @ Fri, 10 Dec 2021 10:32:54: #2 predicted fragment length is 63 bps INFO @ Fri, 10 Dec 2021 10:32:54: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 10 Dec 2021 10:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.10_model.r WARNING @ Fri, 10 Dec 2021 10:32:54: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:32:54: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 10 Dec 2021 10:32:54: #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 10:32:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:32:54: #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 @ Fri, 10 Dec 2021 10:32:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.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 10:32:57: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:32:57: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:33:01: 1000000 INFO @ Fri, 10 Dec 2021 10:33:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:33:06: 2000000 INFO @ Fri, 10 Dec 2021 10:33:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:33:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:33:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.10_summits.bed INFO @ Fri, 10 Dec 2021 10:33:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2105 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:33:11: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:33:16: 4000000 INFO @ Fri, 10 Dec 2021 10:33:19: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:33:19: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:33:19: #1 total tags in treatment: 4511966 INFO @ Fri, 10 Dec 2021 10:33:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:33:19: #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 10:33:19: #1 tags after filtering in treatment: 4511966 INFO @ Fri, 10 Dec 2021 10:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:33:19: #1 finished! INFO @ Fri, 10 Dec 2021 10:33:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:33:19: #2 number of paired peaks: 1839 INFO @ Fri, 10 Dec 2021 10:33:19: start model_add_line... INFO @ Fri, 10 Dec 2021 10:33:19: start X-correlation... INFO @ Fri, 10 Dec 2021 10:33:19: end of X-cor INFO @ Fri, 10 Dec 2021 10:33:19: #2 finished! INFO @ Fri, 10 Dec 2021 10:33:19: #2 predicted fragment length is 63 bps INFO @ Fri, 10 Dec 2021 10:33:19: #2 alternative fragment length(s) may be 63 bps INFO @ Fri, 10 Dec 2021 10:33:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.20_model.r WARNING @ Fri, 10 Dec 2021 10:33:19: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:33:19: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Fri, 10 Dec 2021 10:33:19: #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 10:33:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:33:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:33:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:33:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:33:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:33:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712950/SRX4712950.20_summits.bed INFO @ Fri, 10 Dec 2021 10:33:33: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1187 records, 4 fields): 3 millis CompletedMACS2peakCalling