Job ID = 14168087 SRX = SRX8688979 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16567165 spots for SRR12174348/SRR12174348.sra Written 16567165 spots for SRR12174348/SRR12174348.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168849 ("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: 00:06:01 16567165 reads; of these: 16567165 (100.00%) were unpaired; of these: 688407 (4.16%) aligned 0 times 10480494 (63.26%) aligned exactly 1 time 5398264 (32.58%) aligned >1 times 95.84% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 2378148 / 15878758 = 0.1498 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 15:22:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.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 15:22:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:22:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:22:15: 1000000 INFO @ Fri, 10 Dec 2021 15:22:20: 2000000 INFO @ Fri, 10 Dec 2021 15:22:24: 3000000 INFO @ Fri, 10 Dec 2021 15:22:29: 4000000 INFO @ Fri, 10 Dec 2021 15:22:34: 5000000 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 15:22:39: 6000000 INFO @ Fri, 10 Dec 2021 15:22:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.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 15:22:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:22:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:22:44: 7000000 INFO @ Fri, 10 Dec 2021 15:22:46: 1000000 INFO @ Fri, 10 Dec 2021 15:22:49: 8000000 INFO @ Fri, 10 Dec 2021 15:22:52: 2000000 INFO @ Fri, 10 Dec 2021 15:22:54: 9000000 INFO @ Fri, 10 Dec 2021 15:22:58: 3000000 INFO @ Fri, 10 Dec 2021 15:22:59: 10000000 INFO @ Fri, 10 Dec 2021 15:23:04: 4000000 INFO @ Fri, 10 Dec 2021 15:23:04: 11000000 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 15:23:09: 12000000 INFO @ Fri, 10 Dec 2021 15:23:10: 5000000 INFO @ Fri, 10 Dec 2021 15:23:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.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 15:23:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:23:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:23:15: 13000000 INFO @ Fri, 10 Dec 2021 15:23:16: 6000000 INFO @ Fri, 10 Dec 2021 15:23:16: 1000000 INFO @ Fri, 10 Dec 2021 15:23:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:23:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:23:17: #1 total tags in treatment: 13500610 INFO @ Fri, 10 Dec 2021 15:23:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:23:17: #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 15:23:18: #1 tags after filtering in treatment: 13500610 INFO @ Fri, 10 Dec 2021 15:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:23:18: #1 finished! INFO @ Fri, 10 Dec 2021 15:23:18: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:23:18: #2 number of paired peaks: 488 WARNING @ Fri, 10 Dec 2021 15:23:18: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Fri, 10 Dec 2021 15:23:18: start model_add_line... INFO @ Fri, 10 Dec 2021 15:23:19: start X-correlation... INFO @ Fri, 10 Dec 2021 15:23:19: end of X-cor INFO @ Fri, 10 Dec 2021 15:23:19: #2 finished! INFO @ Fri, 10 Dec 2021 15:23:19: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 15:23:19: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 15:23:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.05_model.r WARNING @ Fri, 10 Dec 2021 15:23:19: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:23:19: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 15:23:19: #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 15:23:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:23:21: 7000000 INFO @ Fri, 10 Dec 2021 15:23:22: 2000000 INFO @ Fri, 10 Dec 2021 15:23:27: 8000000 INFO @ Fri, 10 Dec 2021 15:23:28: 3000000 INFO @ Fri, 10 Dec 2021 15:23:33: 9000000 INFO @ Fri, 10 Dec 2021 15:23:34: 4000000 INFO @ Fri, 10 Dec 2021 15:23:39: 10000000 INFO @ Fri, 10 Dec 2021 15:23:40: 5000000 INFO @ Fri, 10 Dec 2021 15:23:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:23:45: 11000000 INFO @ Fri, 10 Dec 2021 15:23:46: 6000000 INFO @ Fri, 10 Dec 2021 15:23:51: 12000000 INFO @ Fri, 10 Dec 2021 15:23:52: 7000000 INFO @ Fri, 10 Dec 2021 15:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.05_summits.bed INFO @ Fri, 10 Dec 2021 15:23:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14714 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:23:57: 13000000 INFO @ Fri, 10 Dec 2021 15:23:58: 8000000 INFO @ Fri, 10 Dec 2021 15:24:00: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:24:00: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:24:00: #1 total tags in treatment: 13500610 INFO @ Fri, 10 Dec 2021 15:24:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:24:00: #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 15:24:00: #1 tags after filtering in treatment: 13500610 INFO @ Fri, 10 Dec 2021 15:24:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:24:00: #1 finished! INFO @ Fri, 10 Dec 2021 15:24:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:24:01: #2 number of paired peaks: 488 WARNING @ Fri, 10 Dec 2021 15:24:01: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Fri, 10 Dec 2021 15:24:01: start model_add_line... INFO @ Fri, 10 Dec 2021 15:24:01: start X-correlation... INFO @ Fri, 10 Dec 2021 15:24:01: end of X-cor INFO @ Fri, 10 Dec 2021 15:24:01: #2 finished! INFO @ Fri, 10 Dec 2021 15:24:01: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 15:24:01: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 15:24:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.10_model.r WARNING @ Fri, 10 Dec 2021 15:24:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:24:01: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 15:24:01: #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 15:24:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:24:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:24:04: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:24:10: 10000000 INFO @ Fri, 10 Dec 2021 15:24:16: 11000000 INFO @ Fri, 10 Dec 2021 15:24:22: 12000000 INFO @ Fri, 10 Dec 2021 15:24:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:24:28: 13000000 INFO @ Fri, 10 Dec 2021 15:24:31: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:24:31: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:24:31: #1 total tags in treatment: 13500610 INFO @ Fri, 10 Dec 2021 15:24:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:24:31: #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 15:24:31: #1 tags after filtering in treatment: 13500610 INFO @ Fri, 10 Dec 2021 15:24:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:24:31: #1 finished! INFO @ Fri, 10 Dec 2021 15:24:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:24:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:24:32: #2 number of paired peaks: 488 WARNING @ Fri, 10 Dec 2021 15:24:32: Fewer paired peaks (488) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 488 pairs to build model! INFO @ Fri, 10 Dec 2021 15:24:32: start model_add_line... INFO @ Fri, 10 Dec 2021 15:24:32: start X-correlation... INFO @ Fri, 10 Dec 2021 15:24:32: end of X-cor INFO @ Fri, 10 Dec 2021 15:24:32: #2 finished! INFO @ Fri, 10 Dec 2021 15:24:32: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 15:24:32: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 15:24:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.20_model.r WARNING @ Fri, 10 Dec 2021 15:24:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:24:32: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 15:24:32: #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 15:24:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:24:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.10_summits.bed INFO @ Fri, 10 Dec 2021 15:24:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3594 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:24:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:25:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:25:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:25:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688979/SRX8688979.20_summits.bed INFO @ Fri, 10 Dec 2021 15:25:08: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1179 records, 4 fields): 45 millis CompletedMACS2peakCalling