Job ID = 16438134 SRX = SRX10031710 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 86393121 spots for SRR13634480/SRR13634480.sra Written 86393121 spots for SRR13634480/SRR13634480.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439140 ("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: 00:39:18 86393121 reads; of these: 86393121 (100.00%) were unpaired; of these: 46595374 (53.93%) aligned 0 times 32351452 (37.45%) aligned exactly 1 time 7446295 (8.62%) aligned >1 times 46.07% overall alignment rate Time searching: 00:39:18 Overall time: 00:39:18 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 20 files... [bam_rmdupse_core] 16197203 / 39797747 = 0.4070 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 14:41:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.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 14:41:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:41:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:23: 1000000 INFO @ Tue, 02 Aug 2022 14:41:31: 2000000 INFO @ Tue, 02 Aug 2022 14:41:40: 3000000 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 14:41:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.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 14:41:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:41:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:48: 4000000 INFO @ Tue, 02 Aug 2022 14:41:54: 1000000 INFO @ Tue, 02 Aug 2022 14:41:57: 5000000 INFO @ Tue, 02 Aug 2022 14:42:03: 2000000 INFO @ Tue, 02 Aug 2022 14:42:05: 6000000 INFO @ Tue, 02 Aug 2022 14:42:12: 3000000 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 14:42:13: 7000000 INFO @ Tue, 02 Aug 2022 14:42:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.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 14:42:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:42:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:42:22: 4000000 INFO @ Tue, 02 Aug 2022 14:42:23: 8000000 INFO @ Tue, 02 Aug 2022 14:42:25: 1000000 INFO @ Tue, 02 Aug 2022 14:42:31: 5000000 INFO @ Tue, 02 Aug 2022 14:42:31: 9000000 INFO @ Tue, 02 Aug 2022 14:42:33: 2000000 INFO @ Tue, 02 Aug 2022 14:42:40: 6000000 INFO @ Tue, 02 Aug 2022 14:42:40: 10000000 INFO @ Tue, 02 Aug 2022 14:42:41: 3000000 INFO @ Tue, 02 Aug 2022 14:42:48: 7000000 INFO @ Tue, 02 Aug 2022 14:42:49: 4000000 INFO @ Tue, 02 Aug 2022 14:42:49: 11000000 INFO @ Tue, 02 Aug 2022 14:42:56: 8000000 INFO @ Tue, 02 Aug 2022 14:42:57: 5000000 INFO @ Tue, 02 Aug 2022 14:42:58: 12000000 INFO @ Tue, 02 Aug 2022 14:43:03: 9000000 INFO @ Tue, 02 Aug 2022 14:43:05: 6000000 INFO @ Tue, 02 Aug 2022 14:43:07: 13000000 INFO @ Tue, 02 Aug 2022 14:43:11: 10000000 INFO @ Tue, 02 Aug 2022 14:43:13: 7000000 INFO @ Tue, 02 Aug 2022 14:43:15: 14000000 INFO @ Tue, 02 Aug 2022 14:43:18: 11000000 INFO @ Tue, 02 Aug 2022 14:43:21: 8000000 INFO @ Tue, 02 Aug 2022 14:43:23: 15000000 INFO @ Tue, 02 Aug 2022 14:43:25: 12000000 INFO @ Tue, 02 Aug 2022 14:43:28: 9000000 INFO @ Tue, 02 Aug 2022 14:43:32: 16000000 INFO @ Tue, 02 Aug 2022 14:43:32: 13000000 INFO @ Tue, 02 Aug 2022 14:43:36: 10000000 INFO @ Tue, 02 Aug 2022 14:43:40: 17000000 INFO @ Tue, 02 Aug 2022 14:43:40: 14000000 INFO @ Tue, 02 Aug 2022 14:43:44: 11000000 INFO @ Tue, 02 Aug 2022 14:43:48: 18000000 INFO @ Tue, 02 Aug 2022 14:43:48: 15000000 INFO @ Tue, 02 Aug 2022 14:43:51: 12000000 INFO @ Tue, 02 Aug 2022 14:43:56: 19000000 INFO @ Tue, 02 Aug 2022 14:43:56: 16000000 INFO @ Tue, 02 Aug 2022 14:44:00: 13000000 INFO @ Tue, 02 Aug 2022 14:44:04: 20000000 INFO @ Tue, 02 Aug 2022 14:44:04: 17000000 INFO @ Tue, 02 Aug 2022 14:44:08: 14000000 INFO @ Tue, 02 Aug 2022 14:44:11: 21000000 INFO @ Tue, 02 Aug 2022 14:44:12: 18000000 INFO @ Tue, 02 Aug 2022 14:44:16: 15000000 INFO @ Tue, 02 Aug 2022 14:44:19: 22000000 INFO @ Tue, 02 Aug 2022 14:44:20: 19000000 INFO @ Tue, 02 Aug 2022 14:44:24: 16000000 INFO @ Tue, 02 Aug 2022 14:44:27: 20000000 INFO @ Tue, 02 Aug 2022 14:44:28: 23000000 INFO @ Tue, 02 Aug 2022 14:44:31: 17000000 INFO @ Tue, 02 Aug 2022 14:44:33: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:44:33: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:44:33: #1 total tags in treatment: 23600544 INFO @ Tue, 02 Aug 2022 14:44:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:44:33: #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 14:44:33: #1 tags after filtering in treatment: 23600544 INFO @ Tue, 02 Aug 2022 14:44:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:44:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:44:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:44:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:44:34: 21000000 INFO @ Tue, 02 Aug 2022 14:44:35: #2 number of paired peaks: 815 WARNING @ Tue, 02 Aug 2022 14:44:35: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Tue, 02 Aug 2022 14:44:35: start model_add_line... INFO @ Tue, 02 Aug 2022 14:44:35: start X-correlation... INFO @ Tue, 02 Aug 2022 14:44:35: end of X-cor INFO @ Tue, 02 Aug 2022 14:44:35: #2 finished! INFO @ Tue, 02 Aug 2022 14:44:35: #2 predicted fragment length is 23 bps INFO @ Tue, 02 Aug 2022 14:44:35: #2 alternative fragment length(s) may be 23 bps INFO @ Tue, 02 Aug 2022 14:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.05_model.r WARNING @ Tue, 02 Aug 2022 14:44:35: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:44:35: #2 You may need to consider one of the other alternative d(s): 23 WARNING @ Tue, 02 Aug 2022 14:44:35: #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 14:44:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:44:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:44:39: 18000000 INFO @ Tue, 02 Aug 2022 14:44:42: 22000000 INFO @ Tue, 02 Aug 2022 14:44:47: 19000000 INFO @ Tue, 02 Aug 2022 14:44:49: 23000000 INFO @ Tue, 02 Aug 2022 14:44:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:44:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:44:53: #1 total tags in treatment: 23600544 INFO @ Tue, 02 Aug 2022 14:44:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:44:53: #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 14:44:54: #1 tags after filtering in treatment: 23600544 INFO @ Tue, 02 Aug 2022 14:44:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:44:54: #1 finished! INFO @ Tue, 02 Aug 2022 14:44:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:44:55: #2 number of paired peaks: 815 WARNING @ Tue, 02 Aug 2022 14:44:55: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Tue, 02 Aug 2022 14:44:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:44:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:44:56: end of X-cor INFO @ Tue, 02 Aug 2022 14:44:56: #2 finished! INFO @ Tue, 02 Aug 2022 14:44:56: #2 predicted fragment length is 23 bps INFO @ Tue, 02 Aug 2022 14:44:56: #2 alternative fragment length(s) may be 23 bps INFO @ Tue, 02 Aug 2022 14:44:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.10_model.r WARNING @ Tue, 02 Aug 2022 14:44:56: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:44:56: #2 You may need to consider one of the other alternative d(s): 23 WARNING @ Tue, 02 Aug 2022 14:44:56: #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 14:44:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:44:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:44:56: 20000000 INFO @ Tue, 02 Aug 2022 14:45:04: 21000000 INFO @ Tue, 02 Aug 2022 14:45:12: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:45:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:45:20: 23000000 INFO @ Tue, 02 Aug 2022 14:45:25: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:45:25: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:45:25: #1 total tags in treatment: 23600544 INFO @ Tue, 02 Aug 2022 14:45:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:45:25: #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 14:45:25: #1 tags after filtering in treatment: 23600544 INFO @ Tue, 02 Aug 2022 14:45:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:45:25: #1 finished! INFO @ Tue, 02 Aug 2022 14:45:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:45:27: #2 number of paired peaks: 815 WARNING @ Tue, 02 Aug 2022 14:45:27: Fewer paired peaks (815) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 815 pairs to build model! INFO @ Tue, 02 Aug 2022 14:45:27: start model_add_line... INFO @ Tue, 02 Aug 2022 14:45:27: start X-correlation... INFO @ Tue, 02 Aug 2022 14:45:27: end of X-cor INFO @ Tue, 02 Aug 2022 14:45:27: #2 finished! INFO @ Tue, 02 Aug 2022 14:45:27: #2 predicted fragment length is 23 bps INFO @ Tue, 02 Aug 2022 14:45:27: #2 alternative fragment length(s) may be 23 bps INFO @ Tue, 02 Aug 2022 14:45:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.20_model.r WARNING @ Tue, 02 Aug 2022 14:45:27: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:45:27: #2 You may need to consider one of the other alternative d(s): 23 WARNING @ Tue, 02 Aug 2022 14:45:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:45:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:45:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:45:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:45:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:45:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:45:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.05_summits.bed INFO @ Tue, 02 Aug 2022 14:45:35: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13962 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.10_summits.bed INFO @ Tue, 02 Aug 2022 14:45:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7838 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:46:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031710/SRX10031710.20_summits.bed INFO @ Tue, 02 Aug 2022 14:46:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2413 records, 4 fields): 95 millis CompletedMACS2peakCalling BigWig に変換しました。