Job ID = 14168158 SRX = SRX8688981 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21135837 spots for SRR12174350/SRR12174350.sra Written 21135837 spots for SRR12174350/SRR12174350.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168989 ("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: 00:10:55 21135837 reads; of these: 21135837 (100.00%) were unpaired; of these: 605652 (2.87%) aligned 0 times 13563993 (64.18%) aligned exactly 1 time 6966192 (32.96%) aligned >1 times 97.13% overall alignment rate Time searching: 00:10:55 Overall time: 00:10:55 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] 2452192 / 20530185 = 0.1194 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 @ Fri, 10 Dec 2021 16:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.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 @ Fri, 10 Dec 2021 16:05:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:05:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:05:43: 1000000 INFO @ Fri, 10 Dec 2021 16:05:51: 2000000 INFO @ Fri, 10 Dec 2021 16:06:00: 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 @ Fri, 10 Dec 2021 16:06:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.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 @ Fri, 10 Dec 2021 16:06:03: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:06:03: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:06:09: 4000000 INFO @ Fri, 10 Dec 2021 16:06:11: 1000000 INFO @ Fri, 10 Dec 2021 16:06:18: 5000000 INFO @ Fri, 10 Dec 2021 16:06:19: 2000000 INFO @ Fri, 10 Dec 2021 16:06:27: 3000000 INFO @ Fri, 10 Dec 2021 16:06:27: 6000000 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 @ Fri, 10 Dec 2021 16:06:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.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 @ Fri, 10 Dec 2021 16:06:33: #1 read tag files... INFO @ Fri, 10 Dec 2021 16:06:33: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 16:06:35: 4000000 INFO @ Fri, 10 Dec 2021 16:06:36: 7000000 INFO @ Fri, 10 Dec 2021 16:06:42: 1000000 INFO @ Fri, 10 Dec 2021 16:06:44: 5000000 INFO @ Fri, 10 Dec 2021 16:06:45: 8000000 INFO @ Fri, 10 Dec 2021 16:06:50: 2000000 INFO @ Fri, 10 Dec 2021 16:06:52: 6000000 INFO @ Fri, 10 Dec 2021 16:06:54: 9000000 INFO @ Fri, 10 Dec 2021 16:06:59: 3000000 INFO @ Fri, 10 Dec 2021 16:07:00: 7000000 INFO @ Fri, 10 Dec 2021 16:07:04: 10000000 INFO @ Fri, 10 Dec 2021 16:07:07: 4000000 INFO @ Fri, 10 Dec 2021 16:07:09: 8000000 INFO @ Fri, 10 Dec 2021 16:07:13: 11000000 INFO @ Fri, 10 Dec 2021 16:07:16: 5000000 INFO @ Fri, 10 Dec 2021 16:07:18: 9000000 INFO @ Fri, 10 Dec 2021 16:07:22: 12000000 INFO @ Fri, 10 Dec 2021 16:07:25: 6000000 INFO @ Fri, 10 Dec 2021 16:07:27: 10000000 INFO @ Fri, 10 Dec 2021 16:07:31: 13000000 INFO @ Fri, 10 Dec 2021 16:07:34: 7000000 INFO @ Fri, 10 Dec 2021 16:07:36: 11000000 INFO @ Fri, 10 Dec 2021 16:07:41: 14000000 INFO @ Fri, 10 Dec 2021 16:07:43: 8000000 INFO @ Fri, 10 Dec 2021 16:07:45: 12000000 INFO @ Fri, 10 Dec 2021 16:07:50: 15000000 INFO @ Fri, 10 Dec 2021 16:07:53: 9000000 INFO @ Fri, 10 Dec 2021 16:07:54: 13000000 INFO @ Fri, 10 Dec 2021 16:07:59: 16000000 INFO @ Fri, 10 Dec 2021 16:08:02: 10000000 INFO @ Fri, 10 Dec 2021 16:08:03: 14000000 INFO @ Fri, 10 Dec 2021 16:08:09: 17000000 INFO @ Fri, 10 Dec 2021 16:08:11: 11000000 INFO @ Fri, 10 Dec 2021 16:08:12: 15000000 INFO @ Fri, 10 Dec 2021 16:08:18: 18000000 INFO @ Fri, 10 Dec 2021 16:08:19: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:08:19: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:08:19: #1 total tags in treatment: 18077993 INFO @ Fri, 10 Dec 2021 16:08:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:08:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:08:19: #1 tags after filtering in treatment: 18077993 INFO @ Fri, 10 Dec 2021 16:08:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:08:19: #1 finished! INFO @ Fri, 10 Dec 2021 16:08:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:08:20: 12000000 INFO @ Fri, 10 Dec 2021 16:08:21: #2 number of paired peaks: 225 WARNING @ Fri, 10 Dec 2021 16:08:21: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Fri, 10 Dec 2021 16:08:21: start model_add_line... INFO @ Fri, 10 Dec 2021 16:08:21: start X-correlation... INFO @ Fri, 10 Dec 2021 16:08:21: end of X-cor INFO @ Fri, 10 Dec 2021 16:08:21: #2 finished! INFO @ Fri, 10 Dec 2021 16:08:21: #2 predicted fragment length is 43 bps INFO @ Fri, 10 Dec 2021 16:08:21: #2 alternative fragment length(s) may be 43 bps INFO @ Fri, 10 Dec 2021 16:08:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.05_model.r WARNING @ Fri, 10 Dec 2021 16:08:21: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:08:21: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Fri, 10 Dec 2021 16:08:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:08:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:08:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:08:22: 16000000 INFO @ Fri, 10 Dec 2021 16:08:29: 13000000 INFO @ Fri, 10 Dec 2021 16:08:31: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 16:08:38: 14000000 INFO @ Fri, 10 Dec 2021 16:08:40: 18000000 INFO @ Fri, 10 Dec 2021 16:08:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:08:41: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:08:41: #1 total tags in treatment: 18077993 INFO @ Fri, 10 Dec 2021 16:08:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:08:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:08:41: #1 tags after filtering in treatment: 18077993 INFO @ Fri, 10 Dec 2021 16:08:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:08:41: #1 finished! INFO @ Fri, 10 Dec 2021 16:08:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:08:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:08:43: #2 number of paired peaks: 225 WARNING @ Fri, 10 Dec 2021 16:08:43: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Fri, 10 Dec 2021 16:08:43: start model_add_line... INFO @ Fri, 10 Dec 2021 16:08:43: start X-correlation... INFO @ Fri, 10 Dec 2021 16:08:43: end of X-cor INFO @ Fri, 10 Dec 2021 16:08:43: #2 finished! INFO @ Fri, 10 Dec 2021 16:08:43: #2 predicted fragment length is 43 bps INFO @ Fri, 10 Dec 2021 16:08:43: #2 alternative fragment length(s) may be 43 bps INFO @ Fri, 10 Dec 2021 16:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.10_model.r WARNING @ Fri, 10 Dec 2021 16:08:43: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:08:43: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Fri, 10 Dec 2021 16:08:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:08:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 16:08:47: 15000000 INFO @ Fri, 10 Dec 2021 16:08:54: 16000000 INFO @ Fri, 10 Dec 2021 16:09:02: 17000000 INFO @ Fri, 10 Dec 2021 16:09:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:09:10: 18000000 INFO @ Fri, 10 Dec 2021 16:09:11: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 16:09:11: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 16:09:11: #1 total tags in treatment: 18077993 INFO @ Fri, 10 Dec 2021 16:09:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 16:09:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 16:09:11: #1 tags after filtering in treatment: 18077993 INFO @ Fri, 10 Dec 2021 16:09:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 16:09:11: #1 finished! INFO @ Fri, 10 Dec 2021 16:09:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 16:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 16:09:13: #2 number of paired peaks: 225 WARNING @ Fri, 10 Dec 2021 16:09:13: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Fri, 10 Dec 2021 16:09:13: start model_add_line... INFO @ Fri, 10 Dec 2021 16:09:13: start X-correlation... INFO @ Fri, 10 Dec 2021 16:09:13: end of X-cor INFO @ Fri, 10 Dec 2021 16:09:13: #2 finished! INFO @ Fri, 10 Dec 2021 16:09:13: #2 predicted fragment length is 43 bps INFO @ Fri, 10 Dec 2021 16:09:13: #2 alternative fragment length(s) may be 43 bps INFO @ Fri, 10 Dec 2021 16:09:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.20_model.r WARNING @ Fri, 10 Dec 2021 16:09:13: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 16:09:13: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Fri, 10 Dec 2021 16:09:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 16:09:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 16:09:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 16:09:31: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.05_peaks.xls INFO @ Fri, 10 Dec 2021 16:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.05_summits.bed INFO @ Fri, 10 Dec 2021 16:09:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2551 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:09:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.10_peaks.xls INFO @ Fri, 10 Dec 2021 16:09:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:09:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.10_summits.bed INFO @ Fri, 10 Dec 2021 16:09:55: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1556 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 16:10:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 16:10:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.20_peaks.xls INFO @ Fri, 10 Dec 2021 16:10:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 16:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688981/SRX8688981.20_summits.bed INFO @ Fri, 10 Dec 2021 16:10:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1127 records, 4 fields): 7 millis CompletedMACS2peakCalling