Job ID = 12264908 SRX = SRX3088359 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10843 spots for SRR5928037/SRR5928037.sra Written 10843 spots for SRR5928037/SRR5928037.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265014 ("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: 00:00:00 10843 reads; of these: 10843 (100.00%) were unpaired; of these: 5296 (48.84%) aligned 0 times 4306 (39.71%) aligned exactly 1 time 1241 (11.45%) aligned >1 times 51.16% overall alignment rate Time searching: 00:00:00 Overall time: 00:00:00 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] 1434 / 5547 = 0.2585 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 05:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.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 05:57:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:57:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:57:01: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 05:57:01: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 05:57:01: #1 total tags in treatment: 4113 INFO @ Sat, 03 Apr 2021 05:57:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:57:01: #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 05:57:01: #1 tags after filtering in treatment: 4111 INFO @ Sat, 03 Apr 2021 05:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:57:01: #1 finished! INFO @ Sat, 03 Apr 2021 05:57:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:57:01: #2 number of paired peaks: 113 WARNING @ Sat, 03 Apr 2021 05:57:01: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 03 Apr 2021 05:57:01: start model_add_line... INFO @ Sat, 03 Apr 2021 05:57:01: start X-correlation... INFO @ Sat, 03 Apr 2021 05:57:01: end of X-cor INFO @ Sat, 03 Apr 2021 05:57:01: #2 finished! INFO @ Sat, 03 Apr 2021 05:57:01: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Apr 2021 05:57:01: #2 alternative fragment length(s) may be 9,30,48,82,106,124,147,184,199,228,252,298,320,420,475 bps INFO @ Sat, 03 Apr 2021 05:57:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.05_model.r WARNING @ Sat, 03 Apr 2021 05:57:01: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 05:57:01: #2 You may need to consider one of the other alternative d(s): 9,30,48,82,106,124,147,184,199,228,252,298,320,420,475 WARNING @ Sat, 03 Apr 2021 05:57:01: #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 05:57:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 05:57:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 05:57:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.05_peaks.xls INFO @ Sat, 03 Apr 2021 05:57:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 05:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.05_summits.bed INFO @ Sat, 03 Apr 2021 05:57:01: Done! pass1 - making usageList (0 chroms): 8 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 05:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.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 05:57:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:57:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:57:30: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 05:57:30: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 05:57:30: #1 total tags in treatment: 4113 INFO @ Sat, 03 Apr 2021 05:57:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:57:30: #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 05:57:30: #1 tags after filtering in treatment: 4111 INFO @ Sat, 03 Apr 2021 05:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:57:30: #1 finished! INFO @ Sat, 03 Apr 2021 05:57:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:57:30: #2 number of paired peaks: 113 WARNING @ Sat, 03 Apr 2021 05:57:30: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 03 Apr 2021 05:57:30: start model_add_line... INFO @ Sat, 03 Apr 2021 05:57:30: start X-correlation... INFO @ Sat, 03 Apr 2021 05:57:30: end of X-cor INFO @ Sat, 03 Apr 2021 05:57:30: #2 finished! INFO @ Sat, 03 Apr 2021 05:57:30: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Apr 2021 05:57:30: #2 alternative fragment length(s) may be 9,30,48,82,106,124,147,184,199,228,252,298,320,420,475 bps INFO @ Sat, 03 Apr 2021 05:57:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.10_model.r WARNING @ Sat, 03 Apr 2021 05:57:31: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 05:57:31: #2 You may need to consider one of the other alternative d(s): 9,30,48,82,106,124,147,184,199,228,252,298,320,420,475 WARNING @ Sat, 03 Apr 2021 05:57:31: #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 05:57:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:57:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 05:57:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 05:57:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.10_peaks.xls INFO @ Sat, 03 Apr 2021 05:57:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 05:57:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.10_summits.bed INFO @ Sat, 03 Apr 2021 05:57:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 05:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.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 05:58:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 05:58:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 05:58:01: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 05:58:01: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 05:58:01: #1 total tags in treatment: 4113 INFO @ Sat, 03 Apr 2021 05:58:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 05:58:01: #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 05:58:01: #1 tags after filtering in treatment: 4111 INFO @ Sat, 03 Apr 2021 05:58:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 05:58:01: #1 finished! INFO @ Sat, 03 Apr 2021 05:58:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 05:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 05:58:01: #2 number of paired peaks: 113 WARNING @ Sat, 03 Apr 2021 05:58:01: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sat, 03 Apr 2021 05:58:01: start model_add_line... INFO @ Sat, 03 Apr 2021 05:58:01: start X-correlation... INFO @ Sat, 03 Apr 2021 05:58:01: end of X-cor INFO @ Sat, 03 Apr 2021 05:58:01: #2 finished! INFO @ Sat, 03 Apr 2021 05:58:01: #2 predicted fragment length is 124 bps INFO @ Sat, 03 Apr 2021 05:58:01: #2 alternative fragment length(s) may be 9,30,48,82,106,124,147,184,199,228,252,298,320,420,475 bps INFO @ Sat, 03 Apr 2021 05:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.20_model.r WARNING @ Sat, 03 Apr 2021 05:58:01: #2 Since the d (124) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 05:58:01: #2 You may need to consider one of the other alternative d(s): 9,30,48,82,106,124,147,184,199,228,252,298,320,420,475 WARNING @ Sat, 03 Apr 2021 05:58:01: #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 05:58:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 05:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 05:58:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 05:58:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.20_peaks.xls INFO @ Sat, 03 Apr 2021 05:58:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 05:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3088359/SRX3088359.20_summits.bed INFO @ Sat, 03 Apr 2021 05:58:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling