Job ID = 16438597 SRX = SRX10031697 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30847229 spots for SRR13634467/SRR13634467.sra Written 30847229 spots for SRR13634467/SRR13634467.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439006 ("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: 00:18:00 30847229 reads; of these: 30847229 (100.00%) were unpaired; of these: 932122 (3.02%) aligned 0 times 22984754 (74.51%) aligned exactly 1 time 6930353 (22.47%) aligned >1 times 96.98% overall alignment rate Time searching: 00:18:00 Overall time: 00:18:00 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] 5829940 / 29915107 = 0.1949 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 14:31:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.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 14:31:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:31:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:32:07: 1000000 INFO @ Tue, 02 Aug 2022 14:32:20: 2000000 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 14:32:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.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 14:32:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:32:33: 3000000 INFO @ Tue, 02 Aug 2022 14:32:39: 1000000 INFO @ Tue, 02 Aug 2022 14:32:48: 4000000 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 14:32:53: 2000000 INFO @ Tue, 02 Aug 2022 14:32:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.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 14:32:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:33:02: 5000000 INFO @ Tue, 02 Aug 2022 14:33:08: 3000000 INFO @ Tue, 02 Aug 2022 14:33:09: 1000000 INFO @ Tue, 02 Aug 2022 14:33:16: 6000000 INFO @ Tue, 02 Aug 2022 14:33:23: 4000000 INFO @ Tue, 02 Aug 2022 14:33:24: 2000000 INFO @ Tue, 02 Aug 2022 14:33:31: 7000000 INFO @ Tue, 02 Aug 2022 14:33:38: 5000000 INFO @ Tue, 02 Aug 2022 14:33:38: 3000000 INFO @ Tue, 02 Aug 2022 14:33:45: 8000000 INFO @ Tue, 02 Aug 2022 14:33:52: 6000000 INFO @ Tue, 02 Aug 2022 14:33:52: 4000000 INFO @ Tue, 02 Aug 2022 14:34:00: 9000000 INFO @ Tue, 02 Aug 2022 14:34:06: 5000000 INFO @ Tue, 02 Aug 2022 14:34:07: 7000000 INFO @ Tue, 02 Aug 2022 14:34:13: 10000000 INFO @ Tue, 02 Aug 2022 14:34:20: 6000000 INFO @ Tue, 02 Aug 2022 14:34:22: 8000000 INFO @ Tue, 02 Aug 2022 14:34:27: 11000000 INFO @ Tue, 02 Aug 2022 14:34:35: 7000000 INFO @ Tue, 02 Aug 2022 14:34:37: 9000000 INFO @ Tue, 02 Aug 2022 14:34:41: 12000000 INFO @ Tue, 02 Aug 2022 14:34:50: 8000000 INFO @ Tue, 02 Aug 2022 14:34:53: 10000000 INFO @ Tue, 02 Aug 2022 14:34:55: 13000000 INFO @ Tue, 02 Aug 2022 14:35:04: 9000000 INFO @ Tue, 02 Aug 2022 14:35:10: 14000000 INFO @ Tue, 02 Aug 2022 14:35:10: 11000000 INFO @ Tue, 02 Aug 2022 14:35:20: 10000000 INFO @ Tue, 02 Aug 2022 14:35:24: 15000000 INFO @ Tue, 02 Aug 2022 14:35:27: 12000000 INFO @ Tue, 02 Aug 2022 14:35:35: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:35:39: 16000000 INFO @ Tue, 02 Aug 2022 14:35:43: 13000000 INFO @ Tue, 02 Aug 2022 14:35:51: 12000000 INFO @ Tue, 02 Aug 2022 14:35:53: 17000000 INFO @ Tue, 02 Aug 2022 14:35:59: 14000000 INFO @ Tue, 02 Aug 2022 14:36:06: 13000000 INFO @ Tue, 02 Aug 2022 14:36:08: 18000000 INFO @ Tue, 02 Aug 2022 14:36:14: 15000000 INFO @ Tue, 02 Aug 2022 14:36:20: 14000000 INFO @ Tue, 02 Aug 2022 14:36:23: 19000000 INFO @ Tue, 02 Aug 2022 14:36:30: 16000000 INFO @ Tue, 02 Aug 2022 14:36:36: 15000000 INFO @ Tue, 02 Aug 2022 14:36:38: 20000000 INFO @ Tue, 02 Aug 2022 14:36:45: 17000000 INFO @ Tue, 02 Aug 2022 14:36:50: 16000000 INFO @ Tue, 02 Aug 2022 14:36:53: 21000000 INFO @ Tue, 02 Aug 2022 14:37:00: 18000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:37:04: 17000000 INFO @ Tue, 02 Aug 2022 14:37:08: 22000000 INFO @ Tue, 02 Aug 2022 14:37:16: 19000000 INFO @ Tue, 02 Aug 2022 14:37:20: 18000000 INFO @ Tue, 02 Aug 2022 14:37:23: 23000000 INFO @ Tue, 02 Aug 2022 14:37:31: 20000000 INFO @ Tue, 02 Aug 2022 14:37:35: 19000000 INFO @ Tue, 02 Aug 2022 14:37:38: 24000000 INFO @ Tue, 02 Aug 2022 14:37:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:37:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:37:39: #1 total tags in treatment: 24085167 INFO @ Tue, 02 Aug 2022 14:37:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:37:39: #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 14:37:39: #1 tags after filtering in treatment: 24085167 INFO @ Tue, 02 Aug 2022 14:37:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:37:39: #1 finished! INFO @ Tue, 02 Aug 2022 14:37:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:37:41: #2 number of paired peaks: 124 WARNING @ Tue, 02 Aug 2022 14:37:41: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 02 Aug 2022 14:37:41: start model_add_line... INFO @ Tue, 02 Aug 2022 14:37:41: start X-correlation... INFO @ Tue, 02 Aug 2022 14:37:41: end of X-cor INFO @ Tue, 02 Aug 2022 14:37:41: #2 finished! INFO @ Tue, 02 Aug 2022 14:37:41: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:37:41: #2 alternative fragment length(s) may be 1,81,171,191,407,495,516,536,551,591 bps INFO @ Tue, 02 Aug 2022 14:37:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.05_model.r WARNING @ Tue, 02 Aug 2022 14:37:42: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:37:42: #2 You may need to consider one of the other alternative d(s): 1,81,171,191,407,495,516,536,551,591 WARNING @ Tue, 02 Aug 2022 14:37:42: #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 14:37:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:37:46: 21000000 INFO @ Tue, 02 Aug 2022 14:37:49: 20000000 INFO @ Tue, 02 Aug 2022 14:38:01: 22000000 INFO @ Tue, 02 Aug 2022 14:38:04: 21000000 INFO @ Tue, 02 Aug 2022 14:38:16: 23000000 INFO @ Tue, 02 Aug 2022 14:38:19: 22000000 INFO @ Tue, 02 Aug 2022 14:38:31: 24000000 INFO @ Tue, 02 Aug 2022 14:38:32: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:38:32: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:38:32: #1 total tags in treatment: 24085167 INFO @ Tue, 02 Aug 2022 14:38:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:38:32: #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 14:38:32: #1 tags after filtering in treatment: 24085167 INFO @ Tue, 02 Aug 2022 14:38:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:38:32: #1 finished! INFO @ Tue, 02 Aug 2022 14:38:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:38:34: 23000000 INFO @ Tue, 02 Aug 2022 14:38:34: #2 number of paired peaks: 124 WARNING @ Tue, 02 Aug 2022 14:38:34: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 02 Aug 2022 14:38:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:38:35: start X-correlation... INFO @ Tue, 02 Aug 2022 14:38:35: end of X-cor INFO @ Tue, 02 Aug 2022 14:38:35: #2 finished! INFO @ Tue, 02 Aug 2022 14:38:35: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:38:35: #2 alternative fragment length(s) may be 1,81,171,191,407,495,516,536,551,591 bps INFO @ Tue, 02 Aug 2022 14:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.10_model.r WARNING @ Tue, 02 Aug 2022 14:38:35: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:38:35: #2 You may need to consider one of the other alternative d(s): 1,81,171,191,407,495,516,536,551,591 WARNING @ Tue, 02 Aug 2022 14:38:35: #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 14:38:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:38:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:38:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:38:48: 24000000 INFO @ Tue, 02 Aug 2022 14:38:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:38:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:38:49: #1 total tags in treatment: 24085167 INFO @ Tue, 02 Aug 2022 14:38:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:38:49: #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 14:38:49: #1 tags after filtering in treatment: 24085167 INFO @ Tue, 02 Aug 2022 14:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:38:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:38:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:38:51: #2 number of paired peaks: 124 WARNING @ Tue, 02 Aug 2022 14:38:51: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 02 Aug 2022 14:38:51: start model_add_line... INFO @ Tue, 02 Aug 2022 14:38:51: start X-correlation... INFO @ Tue, 02 Aug 2022 14:38:51: end of X-cor INFO @ Tue, 02 Aug 2022 14:38:51: #2 finished! INFO @ Tue, 02 Aug 2022 14:38:51: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:38:51: #2 alternative fragment length(s) may be 1,81,171,191,407,495,516,536,551,591 bps INFO @ Tue, 02 Aug 2022 14:38:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.20_model.r WARNING @ Tue, 02 Aug 2022 14:38:51: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:38:51: #2 You may need to consider one of the other alternative d(s): 1,81,171,191,407,495,516,536,551,591 WARNING @ Tue, 02 Aug 2022 14:38:51: #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 14:38:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:38:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.05_summits.bed INFO @ Tue, 02 Aug 2022 14:39:16: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7078 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:39:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:39:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:40:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:40:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:40:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.10_summits.bed INFO @ Tue, 02 Aug 2022 14:40:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5113 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031697/SRX10031697.20_summits.bed INFO @ Tue, 02 Aug 2022 14:40:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1668 records, 4 fields): 36 millis CompletedMACS2peakCalling