Job ID = 14167065 SRX = SRX7723685 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29202893 spots for SRR11084641/SRR11084641.sra Written 29202893 spots for SRR11084641/SRR11084641.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167488 ("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: 00:14:54 29202893 reads; of these: 29202893 (100.00%) were unpaired; of these: 4223472 (14.46%) aligned 0 times 17892307 (61.27%) aligned exactly 1 time 7087114 (24.27%) aligned >1 times 85.54% overall alignment rate Time searching: 00:14:54 Overall time: 00:14:54 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] 12557699 / 24979421 = 0.5027 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 09:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.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 09:51:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:51:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:51:47: 1000000 INFO @ Fri, 10 Dec 2021 09:51:54: 2000000 INFO @ Fri, 10 Dec 2021 09:52:01: 3000000 INFO @ Fri, 10 Dec 2021 09:52:07: 4000000 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 09:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.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 09:52:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:52:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:52:14: 5000000 INFO @ Fri, 10 Dec 2021 09:52:17: 1000000 INFO @ Fri, 10 Dec 2021 09:52:22: 6000000 INFO @ Fri, 10 Dec 2021 09:52:25: 2000000 INFO @ Fri, 10 Dec 2021 09:52:29: 7000000 INFO @ Fri, 10 Dec 2021 09:52:32: 3000000 INFO @ Fri, 10 Dec 2021 09:52:36: 8000000 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 09:52:40: 4000000 INFO @ Fri, 10 Dec 2021 09:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.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 09:52:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:52:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:52:44: 9000000 INFO @ Fri, 10 Dec 2021 09:52:47: 1000000 INFO @ Fri, 10 Dec 2021 09:52:47: 5000000 INFO @ Fri, 10 Dec 2021 09:52:51: 10000000 INFO @ Fri, 10 Dec 2021 09:52:53: 2000000 INFO @ Fri, 10 Dec 2021 09:52:54: 6000000 INFO @ Fri, 10 Dec 2021 09:52:59: 11000000 INFO @ Fri, 10 Dec 2021 09:53:00: 3000000 INFO @ Fri, 10 Dec 2021 09:53:02: 7000000 INFO @ Fri, 10 Dec 2021 09:53:06: 12000000 INFO @ Fri, 10 Dec 2021 09:53:06: 4000000 INFO @ Fri, 10 Dec 2021 09:53:09: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:53:09: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:53:09: #1 total tags in treatment: 12421722 INFO @ Fri, 10 Dec 2021 09:53:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:53:09: #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 09:53:09: #1 tags after filtering in treatment: 12421722 INFO @ Fri, 10 Dec 2021 09:53:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:53:09: #1 finished! INFO @ Fri, 10 Dec 2021 09:53:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:53:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:53:09: 8000000 INFO @ Fri, 10 Dec 2021 09:53:10: #2 number of paired peaks: 261 WARNING @ Fri, 10 Dec 2021 09:53:10: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 10 Dec 2021 09:53:10: start model_add_line... INFO @ Fri, 10 Dec 2021 09:53:10: start X-correlation... INFO @ Fri, 10 Dec 2021 09:53:10: end of X-cor INFO @ Fri, 10 Dec 2021 09:53:10: #2 finished! INFO @ Fri, 10 Dec 2021 09:53:10: #2 predicted fragment length is 74 bps INFO @ Fri, 10 Dec 2021 09:53:10: #2 alternative fragment length(s) may be 74 bps INFO @ Fri, 10 Dec 2021 09:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05_model.r WARNING @ Fri, 10 Dec 2021 09:53:10: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:53:10: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Fri, 10 Dec 2021 09:53:10: #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 09:53:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:53:13: 5000000 INFO @ Fri, 10 Dec 2021 09:53:17: 9000000 INFO @ Fri, 10 Dec 2021 09:53:19: 6000000 INFO @ Fri, 10 Dec 2021 09:53:24: 10000000 INFO @ Fri, 10 Dec 2021 09:53:26: 7000000 INFO @ Fri, 10 Dec 2021 09:53:32: 11000000 INFO @ Fri, 10 Dec 2021 09:53:32: 8000000 INFO @ Fri, 10 Dec 2021 09:53:34: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:53:39: 9000000 INFO @ Fri, 10 Dec 2021 09:53:39: 12000000 INFO @ Fri, 10 Dec 2021 09:53:42: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:53:42: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:53:42: #1 total tags in treatment: 12421722 INFO @ Fri, 10 Dec 2021 09:53:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:53:42: #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 09:53:42: #1 tags after filtering in treatment: 12421722 INFO @ Fri, 10 Dec 2021 09:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:53:42: #1 finished! INFO @ Fri, 10 Dec 2021 09:53:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:53:43: #2 number of paired peaks: 261 WARNING @ Fri, 10 Dec 2021 09:53:43: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 10 Dec 2021 09:53:43: start model_add_line... INFO @ Fri, 10 Dec 2021 09:53:43: start X-correlation... INFO @ Fri, 10 Dec 2021 09:53:43: end of X-cor INFO @ Fri, 10 Dec 2021 09:53:43: #2 finished! INFO @ Fri, 10 Dec 2021 09:53:43: #2 predicted fragment length is 74 bps INFO @ Fri, 10 Dec 2021 09:53:43: #2 alternative fragment length(s) may be 74 bps INFO @ Fri, 10 Dec 2021 09:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10_model.r WARNING @ Fri, 10 Dec 2021 09:53:43: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:53:43: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Fri, 10 Dec 2021 09:53:43: #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 09:53:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:53:45: 10000000 INFO @ Fri, 10 Dec 2021 09:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.05_summits.bed INFO @ Fri, 10 Dec 2021 09:53:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7168 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:53:51: 11000000 INFO @ Fri, 10 Dec 2021 09:53:57: 12000000 INFO @ Fri, 10 Dec 2021 09:54:00: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:54:00: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:54:00: #1 total tags in treatment: 12421722 INFO @ Fri, 10 Dec 2021 09:54:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:54:00: #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 09:54:00: #1 tags after filtering in treatment: 12421722 INFO @ Fri, 10 Dec 2021 09:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:54:00: #1 finished! INFO @ Fri, 10 Dec 2021 09:54:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:54:01: #2 number of paired peaks: 261 WARNING @ Fri, 10 Dec 2021 09:54:01: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 10 Dec 2021 09:54:01: start model_add_line... INFO @ Fri, 10 Dec 2021 09:54:01: start X-correlation... INFO @ Fri, 10 Dec 2021 09:54:01: end of X-cor INFO @ Fri, 10 Dec 2021 09:54:01: #2 finished! INFO @ Fri, 10 Dec 2021 09:54:01: #2 predicted fragment length is 74 bps INFO @ Fri, 10 Dec 2021 09:54:01: #2 alternative fragment length(s) may be 74 bps INFO @ Fri, 10 Dec 2021 09:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20_model.r WARNING @ Fri, 10 Dec 2021 09:54:01: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:54:01: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Fri, 10 Dec 2021 09:54:01: #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 09:54:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:54:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 09:54:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10_peaks.xls INFO @ Fri, 10 Dec 2021 09:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.10_summits.bed INFO @ Fri, 10 Dec 2021 09:54:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2681 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:54:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20_peaks.xls INFO @ Fri, 10 Dec 2021 09:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723685/SRX7723685.20_summits.bed INFO @ Fri, 10 Dec 2021 09:54:37: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1054 records, 4 fields): 2 millis CompletedMACS2peakCalling