Job ID = 14167287 SRX = SRX8688930 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5806330 spots for SRR12174217/SRR12174217.sra Written 5806330 spots for SRR12174217/SRR12174217.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167911 ("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: 00:01:39 5806330 reads; of these: 5806330 (100.00%) were unpaired; of these: 537055 (9.25%) aligned 0 times 4376231 (75.37%) aligned exactly 1 time 893044 (15.38%) aligned >1 times 90.75% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 180949 / 5269275 = 0.0343 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 11:41:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.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 11:41:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:41:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:41:36: 1000000 INFO @ Fri, 10 Dec 2021 11:41:43: 2000000 INFO @ Fri, 10 Dec 2021 11:41:49: 3000000 INFO @ Fri, 10 Dec 2021 11:41:56: 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 @ Fri, 10 Dec 2021 11:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.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 11:41:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:41:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:42:02: 5000000 INFO @ Fri, 10 Dec 2021 11:42:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:42:03: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:42:03: #1 total tags in treatment: 5088326 INFO @ Fri, 10 Dec 2021 11:42:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:42:03: #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 11:42:03: #1 tags after filtering in treatment: 5088326 INFO @ Fri, 10 Dec 2021 11:42:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:42:03: #1 finished! INFO @ Fri, 10 Dec 2021 11:42:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:42:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:42:03: #2 number of paired peaks: 160 WARNING @ Fri, 10 Dec 2021 11:42:03: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 10 Dec 2021 11:42:03: start model_add_line... INFO @ Fri, 10 Dec 2021 11:42:03: start X-correlation... INFO @ Fri, 10 Dec 2021 11:42:03: end of X-cor INFO @ Fri, 10 Dec 2021 11:42:03: #2 finished! INFO @ Fri, 10 Dec 2021 11:42:03: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 11:42:03: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 11:42:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.05_model.r WARNING @ Fri, 10 Dec 2021 11:42:03: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:42:03: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 11:42:03: #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 11:42:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:42:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:42:06: 1000000 INFO @ Fri, 10 Dec 2021 11:42:12: 2000000 INFO @ Fri, 10 Dec 2021 11:42:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.05_summits.bed INFO @ Fri, 10 Dec 2021 11:42:19: Done! INFO @ Fri, 10 Dec 2021 11:42:19: 3000000 pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1060 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:42:25: 4000000 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 11:42:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.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 11:42:30: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:42:30: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:42:31: 5000000 INFO @ Fri, 10 Dec 2021 11:42:32: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:42:32: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:42:32: #1 total tags in treatment: 5088326 INFO @ Fri, 10 Dec 2021 11:42:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:42:32: #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 11:42:32: #1 tags after filtering in treatment: 5088326 INFO @ Fri, 10 Dec 2021 11:42:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:42:32: #1 finished! INFO @ Fri, 10 Dec 2021 11:42:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:42:32: #2 number of paired peaks: 160 WARNING @ Fri, 10 Dec 2021 11:42:32: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 10 Dec 2021 11:42:32: start model_add_line... INFO @ Fri, 10 Dec 2021 11:42:32: start X-correlation... INFO @ Fri, 10 Dec 2021 11:42:32: end of X-cor INFO @ Fri, 10 Dec 2021 11:42:32: #2 finished! INFO @ Fri, 10 Dec 2021 11:42:32: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 11:42:32: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 11:42:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.10_model.r WARNING @ Fri, 10 Dec 2021 11:42:32: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:42:32: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 11:42:32: #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 11:42:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:42:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:42:36: 1000000 INFO @ Fri, 10 Dec 2021 11:42:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:42:43: 2000000 INFO @ Fri, 10 Dec 2021 11:42:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:42:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:42:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.10_summits.bed INFO @ Fri, 10 Dec 2021 11:42:47: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (793 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:42:50: 3000000 INFO @ Fri, 10 Dec 2021 11:42:57: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:43:04: 5000000 INFO @ Fri, 10 Dec 2021 11:43:04: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:43:04: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:43:04: #1 total tags in treatment: 5088326 INFO @ Fri, 10 Dec 2021 11:43:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:43:04: #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 11:43:04: #1 tags after filtering in treatment: 5088326 INFO @ Fri, 10 Dec 2021 11:43:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:43:04: #1 finished! INFO @ Fri, 10 Dec 2021 11:43:04: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:43:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:43:05: #2 number of paired peaks: 160 WARNING @ Fri, 10 Dec 2021 11:43:05: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Fri, 10 Dec 2021 11:43:05: start model_add_line... INFO @ Fri, 10 Dec 2021 11:43:05: start X-correlation... INFO @ Fri, 10 Dec 2021 11:43:05: end of X-cor INFO @ Fri, 10 Dec 2021 11:43:05: #2 finished! INFO @ Fri, 10 Dec 2021 11:43:05: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 11:43:05: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 11:43:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.20_model.r WARNING @ Fri, 10 Dec 2021 11:43:05: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:43:05: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 11:43:05: #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 11:43:05: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:43:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:43:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:43:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:43:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:43:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688930/SRX8688930.20_summits.bed INFO @ Fri, 10 Dec 2021 11:43:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (443 records, 4 fields): 2 millis CompletedMACS2peakCalling