Job ID = 12265488 SRX = SRX7196649 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9968293 spots for SRR10507711/SRR10507711.sra Written 9968293 spots for SRR10507711/SRR10507711.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265614 ("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: 00:03:05 9968293 reads; of these: 9968293 (100.00%) were unpaired; of these: 1320024 (13.24%) aligned 0 times 5522193 (55.40%) aligned exactly 1 time 3126076 (31.36%) aligned >1 times 86.76% overall alignment rate Time searching: 00:03:05 Overall time: 00:03:05 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] 2374034 / 8648269 = 0.2745 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 07:22:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.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 07:22:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:22:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:22:33: 1000000 INFO @ Sat, 03 Apr 2021 07:22:40: 2000000 INFO @ Sat, 03 Apr 2021 07:22:46: 3000000 INFO @ Sat, 03 Apr 2021 07:22:53: 4000000 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 07:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.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 07:22:56: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:22:56: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:22:59: 5000000 INFO @ Sat, 03 Apr 2021 07:23:03: 1000000 INFO @ Sat, 03 Apr 2021 07:23:06: 6000000 INFO @ Sat, 03 Apr 2021 07:23:08: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:23:08: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:23:08: #1 total tags in treatment: 6274235 INFO @ Sat, 03 Apr 2021 07:23:08: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:23:08: #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 07:23:08: #1 tags after filtering in treatment: 6274235 INFO @ Sat, 03 Apr 2021 07:23:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:23:08: #1 finished! INFO @ Sat, 03 Apr 2021 07:23:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:23:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:23:09: #2 number of paired peaks: 179 WARNING @ Sat, 03 Apr 2021 07:23:09: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 03 Apr 2021 07:23:09: start model_add_line... INFO @ Sat, 03 Apr 2021 07:23:09: start X-correlation... INFO @ Sat, 03 Apr 2021 07:23:09: end of X-cor INFO @ Sat, 03 Apr 2021 07:23:09: #2 finished! INFO @ Sat, 03 Apr 2021 07:23:09: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 07:23:09: #2 alternative fragment length(s) may be 50,531 bps INFO @ Sat, 03 Apr 2021 07:23:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.05_model.r WARNING @ Sat, 03 Apr 2021 07:23:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:23:09: #2 You may need to consider one of the other alternative d(s): 50,531 WARNING @ Sat, 03 Apr 2021 07:23:09: #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 07:23:09: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:23:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:23:10: 2000000 INFO @ Sat, 03 Apr 2021 07:23:17: 3000000 INFO @ Sat, 03 Apr 2021 07:23:23: 4000000 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 07:23:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.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 07:23:26: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:23:26: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:23:30: 5000000 INFO @ Sat, 03 Apr 2021 07:23:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:23:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:23:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.05_summits.bed INFO @ Sat, 03 Apr 2021 07:23:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1275 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:23:32: 1000000 INFO @ Sat, 03 Apr 2021 07:23:36: 6000000 INFO @ Sat, 03 Apr 2021 07:23:38: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:23:38: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:23:38: #1 total tags in treatment: 6274235 INFO @ Sat, 03 Apr 2021 07:23:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:23:38: #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 07:23:38: #1 tags after filtering in treatment: 6274235 INFO @ Sat, 03 Apr 2021 07:23:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:23:38: #1 finished! INFO @ Sat, 03 Apr 2021 07:23:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:23:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:23:38: 2000000 INFO @ Sat, 03 Apr 2021 07:23:39: #2 number of paired peaks: 179 WARNING @ Sat, 03 Apr 2021 07:23:39: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 03 Apr 2021 07:23:39: start model_add_line... INFO @ Sat, 03 Apr 2021 07:23:39: start X-correlation... INFO @ Sat, 03 Apr 2021 07:23:39: end of X-cor INFO @ Sat, 03 Apr 2021 07:23:39: #2 finished! INFO @ Sat, 03 Apr 2021 07:23:39: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 07:23:39: #2 alternative fragment length(s) may be 50,531 bps INFO @ Sat, 03 Apr 2021 07:23:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.10_model.r WARNING @ Sat, 03 Apr 2021 07:23:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:23:39: #2 You may need to consider one of the other alternative d(s): 50,531 WARNING @ Sat, 03 Apr 2021 07:23:39: #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 07:23:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:23:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:23:44: 3000000 INFO @ Sat, 03 Apr 2021 07:23:50: 4000000 INFO @ Sat, 03 Apr 2021 07:23:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:23:55: 5000000 INFO @ Sat, 03 Apr 2021 07:24:01: 6000000 INFO @ Sat, 03 Apr 2021 07:24:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:24:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:24:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.10_summits.bed INFO @ Sat, 03 Apr 2021 07:24:02: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (654 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:24:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:24:02: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:24:02: #1 total tags in treatment: 6274235 INFO @ Sat, 03 Apr 2021 07:24:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:24:02: #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 07:24:02: #1 tags after filtering in treatment: 6274235 INFO @ Sat, 03 Apr 2021 07:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:24:02: #1 finished! INFO @ Sat, 03 Apr 2021 07:24:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:24:03: #2 number of paired peaks: 179 WARNING @ Sat, 03 Apr 2021 07:24:03: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 03 Apr 2021 07:24:03: start model_add_line... INFO @ Sat, 03 Apr 2021 07:24:03: start X-correlation... INFO @ Sat, 03 Apr 2021 07:24:03: end of X-cor INFO @ Sat, 03 Apr 2021 07:24:03: #2 finished! INFO @ Sat, 03 Apr 2021 07:24:03: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 07:24:03: #2 alternative fragment length(s) may be 50,531 bps INFO @ Sat, 03 Apr 2021 07:24:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.20_model.r WARNING @ Sat, 03 Apr 2021 07:24:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:24:03: #2 You may need to consider one of the other alternative d(s): 50,531 WARNING @ Sat, 03 Apr 2021 07:24:03: #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 07:24:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:24:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:24:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:24:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:24:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:24:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7196649/SRX7196649.20_summits.bed INFO @ Sat, 03 Apr 2021 07:24:25: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling