Job ID = 12265397 SRX = SRX7191480 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17895159 spots for SRR10502464/SRR10502464.sra Written 17895159 spots for SRR10502464/SRR10502464.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265517 ("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: 00:05:18 17895159 reads; of these: 17895159 (100.00%) were unpaired; of these: 3598339 (20.11%) aligned 0 times 9046399 (50.55%) aligned exactly 1 time 5250421 (29.34%) aligned >1 times 79.89% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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 8 files... [bam_rmdupse_core] 7636095 / 14296820 = 0.5341 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 06:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.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 06:58:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:58:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:58:33: 1000000 INFO @ Sat, 03 Apr 2021 06:58:40: 2000000 INFO @ Sat, 03 Apr 2021 06:58:48: 3000000 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 06:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.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 06:58:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:58:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:58:56: 4000000 INFO @ Sat, 03 Apr 2021 06:59:03: 1000000 INFO @ Sat, 03 Apr 2021 06:59:04: 5000000 INFO @ Sat, 03 Apr 2021 06:59:12: 2000000 INFO @ Sat, 03 Apr 2021 06:59:13: 6000000 INFO @ Sat, 03 Apr 2021 06:59:19: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:59:19: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:59:19: #1 total tags in treatment: 6660725 INFO @ Sat, 03 Apr 2021 06:59:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:59:19: #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 06:59:19: #1 tags after filtering in treatment: 6660725 INFO @ Sat, 03 Apr 2021 06:59:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:59:19: #1 finished! INFO @ Sat, 03 Apr 2021 06:59:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:59:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:59:19: #2 number of paired peaks: 647 WARNING @ Sat, 03 Apr 2021 06:59:19: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 03 Apr 2021 06:59:19: start model_add_line... INFO @ Sat, 03 Apr 2021 06:59:19: start X-correlation... INFO @ Sat, 03 Apr 2021 06:59:19: end of X-cor INFO @ Sat, 03 Apr 2021 06:59:19: #2 finished! INFO @ Sat, 03 Apr 2021 06:59:19: #2 predicted fragment length is 58 bps INFO @ Sat, 03 Apr 2021 06:59:19: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 03 Apr 2021 06:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.05_model.r WARNING @ Sat, 03 Apr 2021 06:59:19: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:59:19: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 03 Apr 2021 06:59:19: #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 06:59:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:59:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:59:20: 3000000 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 06:59:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.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 06:59:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:59:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:59:28: 4000000 INFO @ Sat, 03 Apr 2021 06:59:33: 1000000 INFO @ Sat, 03 Apr 2021 06:59:36: 5000000 INFO @ Sat, 03 Apr 2021 06:59:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:59:41: 2000000 INFO @ Sat, 03 Apr 2021 06:59:45: 6000000 INFO @ Sat, 03 Apr 2021 06:59:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:59:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:59:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.05_summits.bed INFO @ Sat, 03 Apr 2021 06:59:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2702 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:59:49: 3000000 INFO @ Sat, 03 Apr 2021 06:59:50: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:59:50: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:59:50: #1 total tags in treatment: 6660725 INFO @ Sat, 03 Apr 2021 06:59:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:59:50: #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 06:59:50: #1 tags after filtering in treatment: 6660725 INFO @ Sat, 03 Apr 2021 06:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:59:50: #1 finished! INFO @ Sat, 03 Apr 2021 06:59:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:59:51: #2 number of paired peaks: 647 WARNING @ Sat, 03 Apr 2021 06:59:51: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 03 Apr 2021 06:59:51: start model_add_line... INFO @ Sat, 03 Apr 2021 06:59:51: start X-correlation... INFO @ Sat, 03 Apr 2021 06:59:51: end of X-cor INFO @ Sat, 03 Apr 2021 06:59:51: #2 finished! INFO @ Sat, 03 Apr 2021 06:59:51: #2 predicted fragment length is 58 bps INFO @ Sat, 03 Apr 2021 06:59:51: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 03 Apr 2021 06:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.10_model.r WARNING @ Sat, 03 Apr 2021 06:59:51: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:59:51: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 03 Apr 2021 06:59:51: #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 06:59:51: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:59:56: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:00:03: 5000000 INFO @ Sat, 03 Apr 2021 07:00:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:00:10: 6000000 INFO @ Sat, 03 Apr 2021 07:00:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:00:14: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:00:14: #1 total tags in treatment: 6660725 INFO @ Sat, 03 Apr 2021 07:00:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:00:14: #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 07:00:14: #1 tags after filtering in treatment: 6660725 INFO @ Sat, 03 Apr 2021 07:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:00:14: #1 finished! INFO @ Sat, 03 Apr 2021 07:00:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:00:15: #2 number of paired peaks: 647 WARNING @ Sat, 03 Apr 2021 07:00:15: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 03 Apr 2021 07:00:15: start model_add_line... INFO @ Sat, 03 Apr 2021 07:00:15: start X-correlation... INFO @ Sat, 03 Apr 2021 07:00:15: end of X-cor INFO @ Sat, 03 Apr 2021 07:00:15: #2 finished! INFO @ Sat, 03 Apr 2021 07:00:15: #2 predicted fragment length is 58 bps INFO @ Sat, 03 Apr 2021 07:00:15: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 03 Apr 2021 07:00:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.20_model.r WARNING @ Sat, 03 Apr 2021 07:00:15: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:00:15: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 03 Apr 2021 07:00:15: #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 07:00:15: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:00:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.10_summits.bed INFO @ Sat, 03 Apr 2021 07:00:15: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1255 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:00:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191480/SRX7191480.20_summits.bed INFO @ Sat, 03 Apr 2021 07:00:40: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (606 records, 4 fields): 2 millis CompletedMACS2peakCalling