Job ID = 6626749 SRX = SRX7351014 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26994583 spots for SRR10673644/SRR10673644.sra Written 26994583 spots for SRR10673644/SRR10673644.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627041 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:10 26994583 reads; of these: 26994583 (100.00%) were unpaired; of these: 617766 (2.29%) aligned 0 times 16924268 (62.70%) aligned exactly 1 time 9452549 (35.02%) aligned >1 times 97.71% overall alignment rate Time searching: 00:13:11 Overall time: 00:13:11 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 12 files... [bam_rmdupse_core] 4863586 / 26376817 = 0.1844 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:56:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.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 @ Tue, 14 Jul 2020 08:56:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:56:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:57:05: 1000000 INFO @ Tue, 14 Jul 2020 08:57:12: 2000000 INFO @ Tue, 14 Jul 2020 08:57:19: 3000000 INFO @ Tue, 14 Jul 2020 08:57:26: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:57:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.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 @ Tue, 14 Jul 2020 08:57:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:57:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:57:33: 5000000 INFO @ Tue, 14 Jul 2020 08:57:36: 1000000 INFO @ Tue, 14 Jul 2020 08:57:41: 6000000 INFO @ Tue, 14 Jul 2020 08:57:43: 2000000 INFO @ Tue, 14 Jul 2020 08:57:48: 7000000 INFO @ Tue, 14 Jul 2020 08:57:51: 3000000 INFO @ Tue, 14 Jul 2020 08:57:56: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.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 @ Tue, 14 Jul 2020 08:57:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:57:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:57:59: 4000000 INFO @ Tue, 14 Jul 2020 08:58:04: 9000000 INFO @ Tue, 14 Jul 2020 08:58:06: 1000000 INFO @ Tue, 14 Jul 2020 08:58:07: 5000000 INFO @ Tue, 14 Jul 2020 08:58:12: 10000000 INFO @ Tue, 14 Jul 2020 08:58:14: 2000000 INFO @ Tue, 14 Jul 2020 08:58:14: 6000000 INFO @ Tue, 14 Jul 2020 08:58:20: 11000000 INFO @ Tue, 14 Jul 2020 08:58:22: 3000000 INFO @ Tue, 14 Jul 2020 08:58:22: 7000000 INFO @ Tue, 14 Jul 2020 08:58:27: 12000000 INFO @ Tue, 14 Jul 2020 08:58:30: 4000000 INFO @ Tue, 14 Jul 2020 08:58:30: 8000000 INFO @ Tue, 14 Jul 2020 08:58:35: 13000000 INFO @ Tue, 14 Jul 2020 08:58:37: 5000000 INFO @ Tue, 14 Jul 2020 08:58:38: 9000000 INFO @ Tue, 14 Jul 2020 08:58:43: 14000000 INFO @ Tue, 14 Jul 2020 08:58:45: 6000000 INFO @ Tue, 14 Jul 2020 08:58:46: 10000000 INFO @ Tue, 14 Jul 2020 08:58:51: 15000000 INFO @ Tue, 14 Jul 2020 08:58:53: 7000000 INFO @ Tue, 14 Jul 2020 08:58:54: 11000000 INFO @ Tue, 14 Jul 2020 08:58:59: 16000000 INFO @ Tue, 14 Jul 2020 08:59:01: 8000000 INFO @ Tue, 14 Jul 2020 08:59:01: 12000000 INFO @ Tue, 14 Jul 2020 08:59:07: 17000000 INFO @ Tue, 14 Jul 2020 08:59:08: 9000000 INFO @ Tue, 14 Jul 2020 08:59:09: 13000000 INFO @ Tue, 14 Jul 2020 08:59:14: 18000000 INFO @ Tue, 14 Jul 2020 08:59:16: 10000000 INFO @ Tue, 14 Jul 2020 08:59:17: 14000000 INFO @ Tue, 14 Jul 2020 08:59:22: 19000000 INFO @ Tue, 14 Jul 2020 08:59:24: 11000000 INFO @ Tue, 14 Jul 2020 08:59:24: 15000000 INFO @ Tue, 14 Jul 2020 08:59:30: 20000000 INFO @ Tue, 14 Jul 2020 08:59:32: 12000000 INFO @ Tue, 14 Jul 2020 08:59:32: 16000000 INFO @ Tue, 14 Jul 2020 08:59:38: 21000000 INFO @ Tue, 14 Jul 2020 08:59:39: 13000000 INFO @ Tue, 14 Jul 2020 08:59:40: 17000000 INFO @ Tue, 14 Jul 2020 08:59:42: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:59:42: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:59:42: #1 total tags in treatment: 21513231 INFO @ Tue, 14 Jul 2020 08:59:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:59:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:59:42: #1 tags after filtering in treatment: 21513231 INFO @ Tue, 14 Jul 2020 08:59:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:59:42: #1 finished! INFO @ Tue, 14 Jul 2020 08:59:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:59:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:59:43: #2 number of paired peaks: 497 WARNING @ Tue, 14 Jul 2020 08:59:43: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 14 Jul 2020 08:59:43: start model_add_line... INFO @ Tue, 14 Jul 2020 08:59:44: start X-correlation... INFO @ Tue, 14 Jul 2020 08:59:44: end of X-cor INFO @ Tue, 14 Jul 2020 08:59:44: #2 finished! INFO @ Tue, 14 Jul 2020 08:59:44: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 08:59:44: #2 alternative fragment length(s) may be 2,67,587,593,597 bps INFO @ Tue, 14 Jul 2020 08:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.05_model.r WARNING @ Tue, 14 Jul 2020 08:59:44: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:59:44: #2 You may need to consider one of the other alternative d(s): 2,67,587,593,597 WARNING @ Tue, 14 Jul 2020 08:59:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:59:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:59:46: 14000000 INFO @ Tue, 14 Jul 2020 08:59:48: 18000000 INFO @ Tue, 14 Jul 2020 08:59:52: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:59:55: 19000000 INFO @ Tue, 14 Jul 2020 08:59:59: 16000000 INFO @ Tue, 14 Jul 2020 09:00:03: 20000000 INFO @ Tue, 14 Jul 2020 09:00:06: 17000000 INFO @ Tue, 14 Jul 2020 09:00:10: 21000000 INFO @ Tue, 14 Jul 2020 09:00:13: 18000000 INFO @ Tue, 14 Jul 2020 09:00:14: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:00:14: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:00:14: #1 total tags in treatment: 21513231 INFO @ Tue, 14 Jul 2020 09:00:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:00:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:00:15: #1 tags after filtering in treatment: 21513231 INFO @ Tue, 14 Jul 2020 09:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:00:15: #1 finished! INFO @ Tue, 14 Jul 2020 09:00:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:00:16: #2 number of paired peaks: 497 WARNING @ Tue, 14 Jul 2020 09:00:16: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 14 Jul 2020 09:00:16: start model_add_line... INFO @ Tue, 14 Jul 2020 09:00:16: start X-correlation... INFO @ Tue, 14 Jul 2020 09:00:16: end of X-cor INFO @ Tue, 14 Jul 2020 09:00:16: #2 finished! INFO @ Tue, 14 Jul 2020 09:00:16: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 09:00:16: #2 alternative fragment length(s) may be 2,67,587,593,597 bps INFO @ Tue, 14 Jul 2020 09:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.10_model.r WARNING @ Tue, 14 Jul 2020 09:00:16: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:00:16: #2 You may need to consider one of the other alternative d(s): 2,67,587,593,597 WARNING @ Tue, 14 Jul 2020 09:00:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:00:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:00:20: 19000000 INFO @ Tue, 14 Jul 2020 09:00:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:00:26: 20000000 INFO @ Tue, 14 Jul 2020 09:00:32: 21000000 INFO @ Tue, 14 Jul 2020 09:00:36: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:00:36: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:00:36: #1 total tags in treatment: 21513231 INFO @ Tue, 14 Jul 2020 09:00:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:00:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:00:36: #1 tags after filtering in treatment: 21513231 INFO @ Tue, 14 Jul 2020 09:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:00:36: #1 finished! INFO @ Tue, 14 Jul 2020 09:00:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:00:37: #2 number of paired peaks: 497 WARNING @ Tue, 14 Jul 2020 09:00:37: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Tue, 14 Jul 2020 09:00:37: start model_add_line... INFO @ Tue, 14 Jul 2020 09:00:37: start X-correlation... INFO @ Tue, 14 Jul 2020 09:00:38: end of X-cor INFO @ Tue, 14 Jul 2020 09:00:38: #2 finished! INFO @ Tue, 14 Jul 2020 09:00:38: #2 predicted fragment length is 67 bps INFO @ Tue, 14 Jul 2020 09:00:38: #2 alternative fragment length(s) may be 2,67,587,593,597 bps INFO @ Tue, 14 Jul 2020 09:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.20_model.r WARNING @ Tue, 14 Jul 2020 09:00:38: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:00:38: #2 You may need to consider one of the other alternative d(s): 2,67,587,593,597 WARNING @ Tue, 14 Jul 2020 09:00:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:00:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:00:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:00:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:00:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:00:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.05_summits.bed INFO @ Tue, 14 Jul 2020 09:00:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3106 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:00:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:01:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:01:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:01:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:01:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.10_summits.bed INFO @ Tue, 14 Jul 2020 09:01:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1790 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:01:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351014/SRX7351014.20_summits.bed INFO @ Tue, 14 Jul 2020 09:01:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (940 records, 4 fields): 2 millis CompletedMACS2peakCalling