Job ID = 6626692 SRX = SRX7351007 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25652027 spots for SRR10673637/SRR10673637.sra Written 25652027 spots for SRR10673637/SRR10673637.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626980 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:31 25652027 reads; of these: 25652027 (100.00%) were unpaired; of these: 733626 (2.86%) aligned 0 times 17153338 (66.87%) aligned exactly 1 time 7765063 (30.27%) aligned >1 times 97.14% overall alignment rate Time searching: 00:11:32 Overall time: 00:11:32 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] 3898445 / 24918401 = 0.1564 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 08:38:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.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 08:38:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:38:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:38:21: 1000000 INFO @ Tue, 14 Jul 2020 08:38:27: 2000000 INFO @ Tue, 14 Jul 2020 08:38:33: 3000000 INFO @ Tue, 14 Jul 2020 08:38:39: 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 08:38:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.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 08:38:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:38:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:38:45: 5000000 INFO @ Tue, 14 Jul 2020 08:38:50: 1000000 INFO @ Tue, 14 Jul 2020 08:38:51: 6000000 INFO @ Tue, 14 Jul 2020 08:38:55: 2000000 INFO @ Tue, 14 Jul 2020 08:38:57: 7000000 INFO @ Tue, 14 Jul 2020 08:39:01: 3000000 INFO @ Tue, 14 Jul 2020 08:39:04: 8000000 INFO @ Tue, 14 Jul 2020 08:39:06: 4000000 INFO @ Tue, 14 Jul 2020 08:39:10: 9000000 INFO @ Tue, 14 Jul 2020 08:39:12: 5000000 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 08:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.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 08:39:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:39:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:39:16: 10000000 INFO @ Tue, 14 Jul 2020 08:39:18: 6000000 INFO @ Tue, 14 Jul 2020 08:39:20: 1000000 INFO @ Tue, 14 Jul 2020 08:39:22: 11000000 INFO @ Tue, 14 Jul 2020 08:39:23: 7000000 INFO @ Tue, 14 Jul 2020 08:39:26: 2000000 INFO @ Tue, 14 Jul 2020 08:39:28: 12000000 INFO @ Tue, 14 Jul 2020 08:39:29: 8000000 INFO @ Tue, 14 Jul 2020 08:39:31: 3000000 INFO @ Tue, 14 Jul 2020 08:39:35: 13000000 INFO @ Tue, 14 Jul 2020 08:39:35: 9000000 INFO @ Tue, 14 Jul 2020 08:39:37: 4000000 INFO @ Tue, 14 Jul 2020 08:39:41: 14000000 INFO @ Tue, 14 Jul 2020 08:39:41: 10000000 INFO @ Tue, 14 Jul 2020 08:39:43: 5000000 INFO @ Tue, 14 Jul 2020 08:39:47: 15000000 INFO @ Tue, 14 Jul 2020 08:39:48: 11000000 INFO @ Tue, 14 Jul 2020 08:39:48: 6000000 INFO @ Tue, 14 Jul 2020 08:39:53: 12000000 INFO @ Tue, 14 Jul 2020 08:39:54: 16000000 INFO @ Tue, 14 Jul 2020 08:39:54: 7000000 INFO @ Tue, 14 Jul 2020 08:39:59: 13000000 INFO @ Tue, 14 Jul 2020 08:39:59: 8000000 INFO @ Tue, 14 Jul 2020 08:40:00: 17000000 INFO @ Tue, 14 Jul 2020 08:40:04: 14000000 INFO @ Tue, 14 Jul 2020 08:40:05: 9000000 INFO @ Tue, 14 Jul 2020 08:40:06: 18000000 INFO @ Tue, 14 Jul 2020 08:40:10: 15000000 INFO @ Tue, 14 Jul 2020 08:40:11: 10000000 INFO @ Tue, 14 Jul 2020 08:40:13: 19000000 INFO @ Tue, 14 Jul 2020 08:40:16: 16000000 INFO @ Tue, 14 Jul 2020 08:40:17: 11000000 INFO @ Tue, 14 Jul 2020 08:40:19: 20000000 INFO @ Tue, 14 Jul 2020 08:40:21: 17000000 INFO @ Tue, 14 Jul 2020 08:40:23: 12000000 INFO @ Tue, 14 Jul 2020 08:40:25: 21000000 INFO @ Tue, 14 Jul 2020 08:40:25: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:40:25: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:40:25: #1 total tags in treatment: 21019956 INFO @ Tue, 14 Jul 2020 08:40:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:40:25: #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 08:40:26: #1 tags after filtering in treatment: 21019956 INFO @ Tue, 14 Jul 2020 08:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:40:26: #1 finished! INFO @ Tue, 14 Jul 2020 08:40:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:40:27: 18000000 INFO @ Tue, 14 Jul 2020 08:40:27: #2 number of paired peaks: 609 WARNING @ Tue, 14 Jul 2020 08:40:27: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Tue, 14 Jul 2020 08:40:27: start model_add_line... INFO @ Tue, 14 Jul 2020 08:40:27: start X-correlation... INFO @ Tue, 14 Jul 2020 08:40:27: end of X-cor INFO @ Tue, 14 Jul 2020 08:40:27: #2 finished! INFO @ Tue, 14 Jul 2020 08:40:27: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 08:40:27: #2 alternative fragment length(s) may be 2,63,570,592 bps INFO @ Tue, 14 Jul 2020 08:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.05_model.r WARNING @ Tue, 14 Jul 2020 08:40:27: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:40:27: #2 You may need to consider one of the other alternative d(s): 2,63,570,592 WARNING @ Tue, 14 Jul 2020 08:40:27: #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 08:40:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:40:28: 13000000 INFO @ Tue, 14 Jul 2020 08:40:33: 19000000 INFO @ Tue, 14 Jul 2020 08:40:34: 14000000 INFO @ Tue, 14 Jul 2020 08:40:38: 20000000 INFO @ Tue, 14 Jul 2020 08:40:39: 15000000 INFO @ Tue, 14 Jul 2020 08:40:44: 21000000 INFO @ Tue, 14 Jul 2020 08:40:44: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:40:44: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:40:44: #1 total tags in treatment: 21019956 INFO @ Tue, 14 Jul 2020 08:40:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:40:44: #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 08:40:44: #1 tags after filtering in treatment: 21019956 INFO @ Tue, 14 Jul 2020 08:40:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:40:44: #1 finished! INFO @ Tue, 14 Jul 2020 08:40:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:40:45: 16000000 INFO @ Tue, 14 Jul 2020 08:40:46: #2 number of paired peaks: 609 WARNING @ Tue, 14 Jul 2020 08:40:46: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Tue, 14 Jul 2020 08:40:46: start model_add_line... INFO @ Tue, 14 Jul 2020 08:40:46: start X-correlation... INFO @ Tue, 14 Jul 2020 08:40:46: end of X-cor INFO @ Tue, 14 Jul 2020 08:40:46: #2 finished! INFO @ Tue, 14 Jul 2020 08:40:46: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 08:40:46: #2 alternative fragment length(s) may be 2,63,570,592 bps INFO @ Tue, 14 Jul 2020 08:40:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.10_model.r WARNING @ Tue, 14 Jul 2020 08:40:46: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:40:46: #2 You may need to consider one of the other alternative d(s): 2,63,570,592 WARNING @ Tue, 14 Jul 2020 08:40:46: #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 08:40:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:40:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:40:50: 17000000 INFO @ Tue, 14 Jul 2020 08:40:56: 18000000 INFO @ Tue, 14 Jul 2020 08:41:01: 19000000 INFO @ Tue, 14 Jul 2020 08:41:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:41:06: 20000000 INFO @ Tue, 14 Jul 2020 08:41:12: 21000000 INFO @ Tue, 14 Jul 2020 08:41:12: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:41:12: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:41:12: #1 total tags in treatment: 21019956 INFO @ Tue, 14 Jul 2020 08:41:12: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:41:12: #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 08:41:12: #1 tags after filtering in treatment: 21019956 INFO @ Tue, 14 Jul 2020 08:41:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:41:12: #1 finished! INFO @ Tue, 14 Jul 2020 08:41:12: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:41:14: #2 number of paired peaks: 609 WARNING @ Tue, 14 Jul 2020 08:41:14: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Tue, 14 Jul 2020 08:41:14: start model_add_line... INFO @ Tue, 14 Jul 2020 08:41:14: start X-correlation... INFO @ Tue, 14 Jul 2020 08:41:14: end of X-cor INFO @ Tue, 14 Jul 2020 08:41:14: #2 finished! INFO @ Tue, 14 Jul 2020 08:41:14: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 08:41:14: #2 alternative fragment length(s) may be 2,63,570,592 bps INFO @ Tue, 14 Jul 2020 08:41:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.20_model.r WARNING @ Tue, 14 Jul 2020 08:41:14: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:41:14: #2 You may need to consider one of the other alternative d(s): 2,63,570,592 WARNING @ Tue, 14 Jul 2020 08:41:14: #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 08:41:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:41:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:41:24: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:41:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.05_summits.bed INFO @ Tue, 14 Jul 2020 08:41:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2979 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.10_summits.bed INFO @ Tue, 14 Jul 2020 08:41:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1841 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:41:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:42:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:42:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:42:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351007/SRX7351007.20_summits.bed INFO @ Tue, 14 Jul 2020 08:42:12: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (920 records, 4 fields): 2 millis CompletedMACS2peakCalling