Job ID = 16438598 SRX = SRX10031698 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34901715 spots for SRR13634468/SRR13634468.sra Written 34901715 spots for SRR13634468/SRR13634468.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439002 ("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: 00:17:02 34901715 reads; of these: 34901715 (100.00%) were unpaired; of these: 1405981 (4.03%) aligned 0 times 25148250 (72.05%) aligned exactly 1 time 8347484 (23.92%) aligned >1 times 95.97% overall alignment rate Time searching: 00:17:02 Overall time: 00:17:02 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 16 files... [bam_rmdupse_core] 5237490 / 33495734 = 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.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, 02 Aug 2022 14:30:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:30:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:30:48: 1000000 INFO @ Tue, 02 Aug 2022 14:30:53: 2000000 INFO @ Tue, 02 Aug 2022 14:30:58: 3000000 INFO @ Tue, 02 Aug 2022 14:31:03: 4000000 INFO @ Tue, 02 Aug 2022 14:31:09: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:31:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.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, 02 Aug 2022 14:31:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:31:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:31:14: 6000000 INFO @ Tue, 02 Aug 2022 14:31:17: 1000000 INFO @ Tue, 02 Aug 2022 14:31:20: 7000000 INFO @ Tue, 02 Aug 2022 14:31:23: 2000000 INFO @ Tue, 02 Aug 2022 14:31:25: 8000000 INFO @ Tue, 02 Aug 2022 14:31:28: 3000000 INFO @ Tue, 02 Aug 2022 14:31:31: 9000000 INFO @ Tue, 02 Aug 2022 14:31:34: 4000000 INFO @ Tue, 02 Aug 2022 14:31:36: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:31:40: 5000000 INFO @ Tue, 02 Aug 2022 14:31:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.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, 02 Aug 2022 14:31:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:31:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:31:42: 11000000 INFO @ Tue, 02 Aug 2022 14:31:46: 6000000 INFO @ Tue, 02 Aug 2022 14:31:48: 1000000 INFO @ Tue, 02 Aug 2022 14:31:48: 12000000 INFO @ Tue, 02 Aug 2022 14:31:52: 7000000 INFO @ Tue, 02 Aug 2022 14:31:54: 2000000 INFO @ Tue, 02 Aug 2022 14:31:55: 13000000 INFO @ Tue, 02 Aug 2022 14:31:59: 8000000 INFO @ Tue, 02 Aug 2022 14:32:01: 14000000 INFO @ Tue, 02 Aug 2022 14:32:01: 3000000 INFO @ Tue, 02 Aug 2022 14:32:05: 9000000 INFO @ Tue, 02 Aug 2022 14:32:07: 15000000 INFO @ Tue, 02 Aug 2022 14:32:07: 4000000 INFO @ Tue, 02 Aug 2022 14:32:12: 10000000 INFO @ Tue, 02 Aug 2022 14:32:13: 16000000 INFO @ Tue, 02 Aug 2022 14:32:14: 5000000 INFO @ Tue, 02 Aug 2022 14:32:18: 11000000 INFO @ Tue, 02 Aug 2022 14:32:19: 17000000 INFO @ Tue, 02 Aug 2022 14:32:20: 6000000 INFO @ Tue, 02 Aug 2022 14:32:24: 12000000 INFO @ Tue, 02 Aug 2022 14:32:26: 18000000 INFO @ Tue, 02 Aug 2022 14:32:27: 7000000 INFO @ Tue, 02 Aug 2022 14:32:31: 13000000 INFO @ Tue, 02 Aug 2022 14:32:32: 19000000 INFO @ Tue, 02 Aug 2022 14:32:33: 8000000 INFO @ Tue, 02 Aug 2022 14:32:37: 14000000 INFO @ Tue, 02 Aug 2022 14:32:38: 20000000 INFO @ Tue, 02 Aug 2022 14:32:40: 9000000 INFO @ Tue, 02 Aug 2022 14:32:43: 15000000 INFO @ Tue, 02 Aug 2022 14:32:44: 21000000 INFO @ Tue, 02 Aug 2022 14:32:46: 10000000 INFO @ Tue, 02 Aug 2022 14:32:49: 16000000 INFO @ Tue, 02 Aug 2022 14:32:50: 22000000 INFO @ Tue, 02 Aug 2022 14:32:53: 11000000 INFO @ Tue, 02 Aug 2022 14:32:56: 17000000 INFO @ Tue, 02 Aug 2022 14:32:57: 23000000 INFO @ Tue, 02 Aug 2022 14:32:59: 12000000 INFO @ Tue, 02 Aug 2022 14:33:02: 18000000 INFO @ Tue, 02 Aug 2022 14:33:03: 24000000 INFO @ Tue, 02 Aug 2022 14:33:05: 13000000 INFO @ Tue, 02 Aug 2022 14:33:08: 19000000 INFO @ Tue, 02 Aug 2022 14:33:09: 25000000 INFO @ Tue, 02 Aug 2022 14:33:12: 14000000 INFO @ Tue, 02 Aug 2022 14:33:15: 20000000 INFO @ Tue, 02 Aug 2022 14:33:15: 26000000 INFO @ Tue, 02 Aug 2022 14:33:18: 15000000 INFO @ Tue, 02 Aug 2022 14:33:21: 21000000 INFO @ Tue, 02 Aug 2022 14:33:22: 27000000 INFO @ Tue, 02 Aug 2022 14:33:24: 16000000 INFO @ Tue, 02 Aug 2022 14:33:27: 22000000 INFO @ Tue, 02 Aug 2022 14:33:28: 28000000 INFO @ Tue, 02 Aug 2022 14:33:30: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:33:30: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:33:30: #1 total tags in treatment: 28258244 INFO @ Tue, 02 Aug 2022 14:33:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:33:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:33:30: #1 tags after filtering in treatment: 28258244 INFO @ Tue, 02 Aug 2022 14:33:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:33:30: #1 finished! INFO @ Tue, 02 Aug 2022 14:33:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:33:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:33:31: 17000000 INFO @ Tue, 02 Aug 2022 14:33:32: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 14:33:32: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 14:33:32: start model_add_line... INFO @ Tue, 02 Aug 2022 14:33:32: start X-correlation... INFO @ Tue, 02 Aug 2022 14:33:32: end of X-cor INFO @ Tue, 02 Aug 2022 14:33:32: #2 finished! INFO @ Tue, 02 Aug 2022 14:33:32: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 14:33:32: #2 alternative fragment length(s) may be 2,70 bps INFO @ Tue, 02 Aug 2022 14:33:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.05_model.r WARNING @ Tue, 02 Aug 2022 14:33:32: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:33:32: #2 You may need to consider one of the other alternative d(s): 2,70 WARNING @ Tue, 02 Aug 2022 14:33:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:33:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:33:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:33:33: 23000000 INFO @ Tue, 02 Aug 2022 14:33:36: 18000000 INFO @ Tue, 02 Aug 2022 14:33:38: 24000000 INFO @ Tue, 02 Aug 2022 14:33:42: 19000000 INFO @ Tue, 02 Aug 2022 14:33:44: 25000000 INFO @ Tue, 02 Aug 2022 14:33:47: 20000000 INFO @ Tue, 02 Aug 2022 14:33:50: 26000000 INFO @ Tue, 02 Aug 2022 14:33:53: 21000000 INFO @ Tue, 02 Aug 2022 14:33:55: 27000000 INFO @ Tue, 02 Aug 2022 14:33:59: 22000000 INFO @ Tue, 02 Aug 2022 14:34:01: 28000000 INFO @ Tue, 02 Aug 2022 14:34:03: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:34:03: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:34:03: #1 total tags in treatment: 28258244 INFO @ Tue, 02 Aug 2022 14:34:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:34:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:34:03: #1 tags after filtering in treatment: 28258244 INFO @ Tue, 02 Aug 2022 14:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:34:03: #1 finished! INFO @ Tue, 02 Aug 2022 14:34:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:34:04: 23000000 INFO @ Tue, 02 Aug 2022 14:34:05: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 14:34:05: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 14:34:05: start model_add_line... INFO @ Tue, 02 Aug 2022 14:34:05: start X-correlation... INFO @ Tue, 02 Aug 2022 14:34:05: end of X-cor INFO @ Tue, 02 Aug 2022 14:34:05: #2 finished! INFO @ Tue, 02 Aug 2022 14:34:05: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 14:34:05: #2 alternative fragment length(s) may be 2,70 bps INFO @ Tue, 02 Aug 2022 14:34:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.10_model.r WARNING @ Tue, 02 Aug 2022 14:34:05: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:34:05: #2 You may need to consider one of the other alternative d(s): 2,70 WARNING @ Tue, 02 Aug 2022 14:34:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:34:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:34:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:34:09: 24000000 INFO @ Tue, 02 Aug 2022 14:34:15: 25000000 INFO @ Tue, 02 Aug 2022 14:34:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:34:20: 26000000 INFO @ Tue, 02 Aug 2022 14:34:25: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:34:31: 28000000 INFO @ Tue, 02 Aug 2022 14:34:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:34:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:34:32: #1 total tags in treatment: 28258244 INFO @ Tue, 02 Aug 2022 14:34:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:34:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:34:33: #1 tags after filtering in treatment: 28258244 INFO @ Tue, 02 Aug 2022 14:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:34:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:34:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:34:35: #2 number of paired peaks: 181 WARNING @ Tue, 02 Aug 2022 14:34:35: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Tue, 02 Aug 2022 14:34:35: start model_add_line... INFO @ Tue, 02 Aug 2022 14:34:35: start X-correlation... INFO @ Tue, 02 Aug 2022 14:34:35: end of X-cor INFO @ Tue, 02 Aug 2022 14:34:35: #2 finished! INFO @ Tue, 02 Aug 2022 14:34:35: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 14:34:35: #2 alternative fragment length(s) may be 2,70 bps INFO @ Tue, 02 Aug 2022 14:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.20_model.r WARNING @ Tue, 02 Aug 2022 14:34:35: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:34:35: #2 You may need to consider one of the other alternative d(s): 2,70 WARNING @ Tue, 02 Aug 2022 14:34:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:34:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.05_summits.bed INFO @ Tue, 02 Aug 2022 14:34:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8575 records, 4 fields): 78 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:34:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:35:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:35:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:35:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.10_summits.bed INFO @ Tue, 02 Aug 2022 14:35:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6415 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:35:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:35:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:35:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:35:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031698/SRX10031698.20_summits.bed INFO @ Tue, 02 Aug 2022 14:35:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4302 records, 4 fields): 20 millis CompletedMACS2peakCalling BigWig に変換しました。