Job ID = 12265300 SRX = SRX5010759 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19123450 spots for SRR8191184/SRR8191184.sra Written 19123450 spots for SRR8191184/SRR8191184.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265446 ("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: 00:08:13 19123450 reads; of these: 19123450 (100.00%) were unpaired; of these: 596210 (3.12%) aligned 0 times 8282958 (43.31%) aligned exactly 1 time 10244282 (53.57%) aligned >1 times 96.88% overall alignment rate Time searching: 00:08:13 Overall time: 00:08:13 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] 10337981 / 18527240 = 0.5580 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 06:42:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.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 06:42:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:42:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:42:20: 1000000 INFO @ Sat, 03 Apr 2021 06:42:30: 2000000 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 06:42:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.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 06:42:39: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:42:39: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:42:40: 3000000 INFO @ Sat, 03 Apr 2021 06:42:48: 1000000 INFO @ Sat, 03 Apr 2021 06:42:50: 4000000 INFO @ Sat, 03 Apr 2021 06:42:58: 2000000 INFO @ Sat, 03 Apr 2021 06:43:00: 5000000 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 06:43:07: 3000000 INFO @ Sat, 03 Apr 2021 06:43:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.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 06:43:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:10: 6000000 INFO @ Sat, 03 Apr 2021 06:43:16: 4000000 INFO @ Sat, 03 Apr 2021 06:43:20: 1000000 INFO @ Sat, 03 Apr 2021 06:43:20: 7000000 INFO @ Sat, 03 Apr 2021 06:43:25: 5000000 INFO @ Sat, 03 Apr 2021 06:43:30: 2000000 INFO @ Sat, 03 Apr 2021 06:43:30: 8000000 INFO @ Sat, 03 Apr 2021 06:43:32: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:43:32: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:43:32: #1 total tags in treatment: 8189259 INFO @ Sat, 03 Apr 2021 06:43:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:43:32: #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 06:43:32: #1 tags after filtering in treatment: 8189259 INFO @ Sat, 03 Apr 2021 06:43:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:43:32: #1 finished! INFO @ Sat, 03 Apr 2021 06:43:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:43:33: #2 number of paired peaks: 309 WARNING @ Sat, 03 Apr 2021 06:43:33: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sat, 03 Apr 2021 06:43:33: start model_add_line... INFO @ Sat, 03 Apr 2021 06:43:33: start X-correlation... INFO @ Sat, 03 Apr 2021 06:43:33: end of X-cor INFO @ Sat, 03 Apr 2021 06:43:33: #2 finished! INFO @ Sat, 03 Apr 2021 06:43:33: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 06:43:33: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 03 Apr 2021 06:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.05_model.r WARNING @ Sat, 03 Apr 2021 06:43:33: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:43:33: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 03 Apr 2021 06:43:33: #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 06:43:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:43:34: 6000000 INFO @ Sat, 03 Apr 2021 06:43:38: 3000000 INFO @ Sat, 03 Apr 2021 06:43:43: 7000000 INFO @ Sat, 03 Apr 2021 06:43:47: 4000000 INFO @ Sat, 03 Apr 2021 06:43:52: 8000000 INFO @ Sat, 03 Apr 2021 06:43:54: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:43:54: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:43:54: #1 total tags in treatment: 8189259 INFO @ Sat, 03 Apr 2021 06:43:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:43:54: #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 06:43:54: #1 tags after filtering in treatment: 8189259 INFO @ Sat, 03 Apr 2021 06:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:43:54: #1 finished! INFO @ Sat, 03 Apr 2021 06:43:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:43:55: #2 number of paired peaks: 309 WARNING @ Sat, 03 Apr 2021 06:43:55: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sat, 03 Apr 2021 06:43:55: start model_add_line... INFO @ Sat, 03 Apr 2021 06:43:55: start X-correlation... INFO @ Sat, 03 Apr 2021 06:43:55: end of X-cor INFO @ Sat, 03 Apr 2021 06:43:55: #2 finished! INFO @ Sat, 03 Apr 2021 06:43:55: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 06:43:55: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 03 Apr 2021 06:43:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.10_model.r WARNING @ Sat, 03 Apr 2021 06:43:55: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:43:55: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 03 Apr 2021 06:43:55: #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 06:43:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:43:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:43:55: 5000000 INFO @ Sat, 03 Apr 2021 06:43:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:44:04: 6000000 INFO @ Sat, 03 Apr 2021 06:44:12: 7000000 INFO @ Sat, 03 Apr 2021 06:44:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:44:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:44:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.05_summits.bed INFO @ Sat, 03 Apr 2021 06:44:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3116 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:44:21: 8000000 INFO @ Sat, 03 Apr 2021 06:44:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:44:22: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:44:22: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:44:22: #1 total tags in treatment: 8189259 INFO @ Sat, 03 Apr 2021 06:44:22: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:44:22: #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 06:44:22: #1 tags after filtering in treatment: 8189259 INFO @ Sat, 03 Apr 2021 06:44:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:44:22: #1 finished! INFO @ Sat, 03 Apr 2021 06:44:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:44:23: #2 number of paired peaks: 309 WARNING @ Sat, 03 Apr 2021 06:44:23: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sat, 03 Apr 2021 06:44:23: start model_add_line... INFO @ Sat, 03 Apr 2021 06:44:23: start X-correlation... INFO @ Sat, 03 Apr 2021 06:44:23: end of X-cor INFO @ Sat, 03 Apr 2021 06:44:23: #2 finished! INFO @ Sat, 03 Apr 2021 06:44:23: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 06:44:23: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 03 Apr 2021 06:44:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.20_model.r WARNING @ Sat, 03 Apr 2021 06:44:23: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:44:23: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 03 Apr 2021 06:44:23: #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 06:44:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:44:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:44:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:44:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:44:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.10_summits.bed INFO @ Sat, 03 Apr 2021 06:44:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (971 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:44:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010759/SRX5010759.20_summits.bed INFO @ Sat, 03 Apr 2021 06:45:03: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 3 millis CompletedMACS2peakCalling