Job ID = 14170383 SRX = SRX8689007 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20333018 spots for SRR12174296/SRR12174296.sra Written 20333018 spots for SRR12174296/SRR12174296.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170792 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:06 20333018 reads; of these: 20333018 (100.00%) were unpaired; of these: 543899 (2.67%) aligned 0 times 13333851 (65.58%) aligned exactly 1 time 6455268 (31.75%) aligned >1 times 97.33% overall alignment rate Time searching: 00:09:07 Overall time: 00:09:07 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] 2169082 / 19789119 = 0.1096 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.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 @ Sat, 11 Dec 2021 06:47:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:29: 1000000 INFO @ Sat, 11 Dec 2021 06:47:38: 2000000 INFO @ Sat, 11 Dec 2021 06:47:46: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.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 @ Sat, 11 Dec 2021 06:47:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:47:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:47:55: 4000000 INFO @ Sat, 11 Dec 2021 06:47:59: 1000000 INFO @ Sat, 11 Dec 2021 06:48:03: 5000000 INFO @ Sat, 11 Dec 2021 06:48:07: 2000000 INFO @ Sat, 11 Dec 2021 06:48:10: 6000000 INFO @ Sat, 11 Dec 2021 06:48:16: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 06:48:18: 7000000 INFO @ Sat, 11 Dec 2021 06:48:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.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 @ Sat, 11 Dec 2021 06:48:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:48:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:48:25: 4000000 INFO @ Sat, 11 Dec 2021 06:48:25: 8000000 INFO @ Sat, 11 Dec 2021 06:48:30: 1000000 INFO @ Sat, 11 Dec 2021 06:48:33: 9000000 INFO @ Sat, 11 Dec 2021 06:48:34: 5000000 INFO @ Sat, 11 Dec 2021 06:48:39: 2000000 INFO @ Sat, 11 Dec 2021 06:48:42: 10000000 INFO @ Sat, 11 Dec 2021 06:48:44: 6000000 INFO @ Sat, 11 Dec 2021 06:48:49: 3000000 INFO @ Sat, 11 Dec 2021 06:48:50: 11000000 INFO @ Sat, 11 Dec 2021 06:48:53: 7000000 INFO @ Sat, 11 Dec 2021 06:48:57: 12000000 INFO @ Sat, 11 Dec 2021 06:48:58: 4000000 INFO @ Sat, 11 Dec 2021 06:49:02: 8000000 INFO @ Sat, 11 Dec 2021 06:49:06: 13000000 INFO @ Sat, 11 Dec 2021 06:49:08: 5000000 INFO @ Sat, 11 Dec 2021 06:49:12: 9000000 INFO @ Sat, 11 Dec 2021 06:49:13: 14000000 INFO @ Sat, 11 Dec 2021 06:49:17: 6000000 INFO @ Sat, 11 Dec 2021 06:49:20: 10000000 INFO @ Sat, 11 Dec 2021 06:49:21: 15000000 INFO @ Sat, 11 Dec 2021 06:49:26: 7000000 INFO @ Sat, 11 Dec 2021 06:49:30: 16000000 INFO @ Sat, 11 Dec 2021 06:49:30: 11000000 INFO @ Sat, 11 Dec 2021 06:49:36: 8000000 INFO @ Sat, 11 Dec 2021 06:49:37: 17000000 INFO @ Sat, 11 Dec 2021 06:49:39: 12000000 INFO @ Sat, 11 Dec 2021 06:49:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:49:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:49:42: #1 total tags in treatment: 17620037 INFO @ Sat, 11 Dec 2021 06:49:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:49:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:49:42: #1 tags after filtering in treatment: 17620037 INFO @ Sat, 11 Dec 2021 06:49:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:49:42: #1 finished! INFO @ Sat, 11 Dec 2021 06:49:42: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:49:43: #2 number of paired peaks: 206 WARNING @ Sat, 11 Dec 2021 06:49:43: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 11 Dec 2021 06:49:43: start model_add_line... INFO @ Sat, 11 Dec 2021 06:49:43: start X-correlation... INFO @ Sat, 11 Dec 2021 06:49:43: end of X-cor INFO @ Sat, 11 Dec 2021 06:49:43: #2 finished! INFO @ Sat, 11 Dec 2021 06:49:43: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 06:49:43: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:49:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.05_model.r WARNING @ Sat, 11 Dec 2021 06:49:43: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:49:43: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 11 Dec 2021 06:49:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:49:43: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:49:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:49:45: 9000000 INFO @ Sat, 11 Dec 2021 06:49:49: 13000000 INFO @ Sat, 11 Dec 2021 06:49:55: 10000000 INFO @ Sat, 11 Dec 2021 06:49:59: 14000000 INFO @ Sat, 11 Dec 2021 06:50:04: 11000000 INFO @ Sat, 11 Dec 2021 06:50:08: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:50:13: 12000000 INFO @ Sat, 11 Dec 2021 06:50:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:50:17: 16000000 INFO @ Sat, 11 Dec 2021 06:50:22: 13000000 INFO @ Sat, 11 Dec 2021 06:50:26: 17000000 INFO @ Sat, 11 Dec 2021 06:50:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:50:31: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:50:31: #1 total tags in treatment: 17620037 INFO @ Sat, 11 Dec 2021 06:50:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:50:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:50:31: 14000000 INFO @ Sat, 11 Dec 2021 06:50:31: #1 tags after filtering in treatment: 17620037 INFO @ Sat, 11 Dec 2021 06:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:50:31: #1 finished! INFO @ Sat, 11 Dec 2021 06:50:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:50:32: #2 number of paired peaks: 206 WARNING @ Sat, 11 Dec 2021 06:50:32: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 11 Dec 2021 06:50:32: start model_add_line... INFO @ Sat, 11 Dec 2021 06:50:32: start X-correlation... INFO @ Sat, 11 Dec 2021 06:50:32: end of X-cor INFO @ Sat, 11 Dec 2021 06:50:32: #2 finished! INFO @ Sat, 11 Dec 2021 06:50:32: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 06:50:32: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.10_model.r WARNING @ Sat, 11 Dec 2021 06:50:32: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:50:32: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 11 Dec 2021 06:50:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:50:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.05_summits.bed INFO @ Sat, 11 Dec 2021 06:50:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2281 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:50:39: 15000000 INFO @ Sat, 11 Dec 2021 06:50:47: 16000000 INFO @ Sat, 11 Dec 2021 06:50:55: 17000000 INFO @ Sat, 11 Dec 2021 06:51:00: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:51:00: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:51:00: #1 total tags in treatment: 17620037 INFO @ Sat, 11 Dec 2021 06:51:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:51:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 06:51:00: #1 tags after filtering in treatment: 17620037 INFO @ Sat, 11 Dec 2021 06:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:51:00: #1 finished! INFO @ Sat, 11 Dec 2021 06:51:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:51:02: #2 number of paired peaks: 206 WARNING @ Sat, 11 Dec 2021 06:51:02: Fewer paired peaks (206) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 206 pairs to build model! INFO @ Sat, 11 Dec 2021 06:51:02: start model_add_line... INFO @ Sat, 11 Dec 2021 06:51:02: start X-correlation... INFO @ Sat, 11 Dec 2021 06:51:02: end of X-cor INFO @ Sat, 11 Dec 2021 06:51:02: #2 finished! INFO @ Sat, 11 Dec 2021 06:51:02: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 06:51:02: #2 alternative fragment length(s) may be 44 bps INFO @ Sat, 11 Dec 2021 06:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.20_model.r WARNING @ Sat, 11 Dec 2021 06:51:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:51:02: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Sat, 11 Dec 2021 06:51:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:51:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:51:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.10_summits.bed INFO @ Sat, 11 Dec 2021 06:51:22: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (1502 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:51:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689007/SRX8689007.20_summits.bed INFO @ Sat, 11 Dec 2021 06:51:51: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1087 records, 4 fields): 5 millis CompletedMACS2peakCalling