Job ID = 16438110 SRX = SRX10031708 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34116987 spots for SRR13634478/SRR13634478.sra Written 34116987 spots for SRR13634478/SRR13634478.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438588 ("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: 00:16:50 34116987 reads; of these: 34116987 (100.00%) were unpaired; of these: 1568149 (4.60%) aligned 0 times 23528209 (68.96%) aligned exactly 1 time 9020629 (26.44%) aligned >1 times 95.40% overall alignment rate Time searching: 00:16:50 Overall time: 00:16:50 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] 9556715 / 32548838 = 0.2936 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 14:06:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.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 14:06:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:06:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:06:10: 1000000 INFO @ Tue, 02 Aug 2022 14:06:16: 2000000 INFO @ Tue, 02 Aug 2022 14:06:22: 3000000 INFO @ Tue, 02 Aug 2022 14:06:28: 4000000 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 14:06:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.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 14:06:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:06:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:06:34: 5000000 INFO @ Tue, 02 Aug 2022 14:06:40: 6000000 INFO @ Tue, 02 Aug 2022 14:06:41: 1000000 INFO @ Tue, 02 Aug 2022 14:06:46: 7000000 INFO @ Tue, 02 Aug 2022 14:06:49: 2000000 INFO @ Tue, 02 Aug 2022 14:06:53: 8000000 INFO @ Tue, 02 Aug 2022 14:06:56: 3000000 INFO @ Tue, 02 Aug 2022 14:06:59: 9000000 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 14:07:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.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 14:07:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:07:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:07:05: 4000000 INFO @ Tue, 02 Aug 2022 14:07:10: 10000000 INFO @ Tue, 02 Aug 2022 14:07:12: 1000000 INFO @ Tue, 02 Aug 2022 14:07:15: 5000000 INFO @ Tue, 02 Aug 2022 14:07:19: 11000000 INFO @ Tue, 02 Aug 2022 14:07:19: 2000000 INFO @ Tue, 02 Aug 2022 14:07:22: 6000000 INFO @ Tue, 02 Aug 2022 14:07:25: 3000000 INFO @ Tue, 02 Aug 2022 14:07:26: 12000000 INFO @ Tue, 02 Aug 2022 14:07:30: 7000000 INFO @ Tue, 02 Aug 2022 14:07:31: 4000000 INFO @ Tue, 02 Aug 2022 14:07:33: 13000000 INFO @ Tue, 02 Aug 2022 14:07:38: 5000000 INFO @ Tue, 02 Aug 2022 14:07:38: 8000000 INFO @ Tue, 02 Aug 2022 14:07:40: 14000000 INFO @ Tue, 02 Aug 2022 14:07:44: 6000000 INFO @ Tue, 02 Aug 2022 14:07:46: 9000000 INFO @ Tue, 02 Aug 2022 14:07:47: 15000000 INFO @ Tue, 02 Aug 2022 14:07:51: 7000000 INFO @ Tue, 02 Aug 2022 14:07:53: 10000000 INFO @ Tue, 02 Aug 2022 14:07:55: 16000000 INFO @ Tue, 02 Aug 2022 14:07:57: 8000000 INFO @ Tue, 02 Aug 2022 14:08:01: 11000000 INFO @ Tue, 02 Aug 2022 14:08:03: 17000000 INFO @ Tue, 02 Aug 2022 14:08:04: 9000000 INFO @ Tue, 02 Aug 2022 14:08:08: 12000000 INFO @ Tue, 02 Aug 2022 14:08:10: 10000000 INFO @ Tue, 02 Aug 2022 14:08:11: 18000000 INFO @ Tue, 02 Aug 2022 14:08:16: 13000000 INFO @ Tue, 02 Aug 2022 14:08:16: 11000000 INFO @ Tue, 02 Aug 2022 14:08:19: 19000000 INFO @ Tue, 02 Aug 2022 14:08:22: 12000000 INFO @ Tue, 02 Aug 2022 14:08:24: 14000000 INFO @ Tue, 02 Aug 2022 14:08:26: 20000000 INFO @ Tue, 02 Aug 2022 14:08:28: 13000000 INFO @ Tue, 02 Aug 2022 14:08:31: 15000000 INFO @ Tue, 02 Aug 2022 14:08:34: 21000000 INFO @ Tue, 02 Aug 2022 14:08:34: 14000000 INFO @ Tue, 02 Aug 2022 14:08:39: 16000000 INFO @ Tue, 02 Aug 2022 14:08:40: 15000000 INFO @ Tue, 02 Aug 2022 14:08:41: 22000000 INFO @ Tue, 02 Aug 2022 14:08:46: 17000000 INFO @ Tue, 02 Aug 2022 14:08:47: 16000000 INFO @ Tue, 02 Aug 2022 14:08:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:08:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:08:49: #1 total tags in treatment: 22992123 INFO @ Tue, 02 Aug 2022 14:08:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:08:49: #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 14:08:49: #1 tags after filtering in treatment: 22992123 INFO @ Tue, 02 Aug 2022 14:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:08:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:08:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:08:51: #2 number of paired peaks: 819 WARNING @ Tue, 02 Aug 2022 14:08:51: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Tue, 02 Aug 2022 14:08:51: start model_add_line... INFO @ Tue, 02 Aug 2022 14:08:51: start X-correlation... INFO @ Tue, 02 Aug 2022 14:08:51: end of X-cor INFO @ Tue, 02 Aug 2022 14:08:51: #2 finished! INFO @ Tue, 02 Aug 2022 14:08:51: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 14:08:51: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 14:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.05_model.r WARNING @ Tue, 02 Aug 2022 14:08:51: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:08:51: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 14:08:51: #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 14:08:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:08:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:08:53: 17000000 INFO @ Tue, 02 Aug 2022 14:08:54: 18000000 INFO @ Tue, 02 Aug 2022 14:08:58: 18000000 INFO @ Tue, 02 Aug 2022 14:09:01: 19000000 INFO @ Tue, 02 Aug 2022 14:09:04: 19000000 INFO @ Tue, 02 Aug 2022 14:09:08: 20000000 INFO @ Tue, 02 Aug 2022 14:09:10: 20000000 INFO @ Tue, 02 Aug 2022 14:09:15: 21000000 INFO @ Tue, 02 Aug 2022 14:09:16: 21000000 INFO @ Tue, 02 Aug 2022 14:09:22: 22000000 INFO @ Tue, 02 Aug 2022 14:09:22: 22000000 INFO @ Tue, 02 Aug 2022 14:09:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:09:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:09:27: #1 total tags in treatment: 22992123 INFO @ Tue, 02 Aug 2022 14:09:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:09:27: #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 14:09:28: #1 tags after filtering in treatment: 22992123 INFO @ Tue, 02 Aug 2022 14:09:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:09:28: #1 finished! INFO @ Tue, 02 Aug 2022 14:09:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:09:28: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:09:28: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:09:28: #1 total tags in treatment: 22992123 INFO @ Tue, 02 Aug 2022 14:09:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:09:28: #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 14:09:29: #1 tags after filtering in treatment: 22992123 INFO @ Tue, 02 Aug 2022 14:09:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:09:29: #1 finished! INFO @ Tue, 02 Aug 2022 14:09:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:09:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:09:29: #2 number of paired peaks: 819 WARNING @ Tue, 02 Aug 2022 14:09:29: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Tue, 02 Aug 2022 14:09:29: start model_add_line... INFO @ Tue, 02 Aug 2022 14:09:30: start X-correlation... INFO @ Tue, 02 Aug 2022 14:09:30: end of X-cor INFO @ Tue, 02 Aug 2022 14:09:30: #2 finished! INFO @ Tue, 02 Aug 2022 14:09:30: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 14:09:30: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 14:09:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.20_model.r WARNING @ Tue, 02 Aug 2022 14:09:30: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:09:30: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 14:09:30: #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 14:09:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:09:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:09:30: #2 number of paired peaks: 819 WARNING @ Tue, 02 Aug 2022 14:09:30: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Tue, 02 Aug 2022 14:09:30: start model_add_line... INFO @ Tue, 02 Aug 2022 14:09:30: start X-correlation... INFO @ Tue, 02 Aug 2022 14:09:30: end of X-cor INFO @ Tue, 02 Aug 2022 14:09:30: #2 finished! INFO @ Tue, 02 Aug 2022 14:09:30: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 14:09:30: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 14:09:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.10_model.r WARNING @ Tue, 02 Aug 2022 14:09:31: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:09:31: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 14:09:31: #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 14:09:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:09:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.05_summits.bed INFO @ Tue, 02 Aug 2022 14:09:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10444 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:10:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:10:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:10:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.20_summits.bed INFO @ Tue, 02 Aug 2022 14:10:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4832 records, 4 fields): 74 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:10:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:10:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:10:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031708/SRX10031708.10_summits.bed INFO @ Tue, 02 Aug 2022 14:10:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7472 records, 4 fields): 62 millis CompletedMACS2peakCalling BigWig に変換しました。