Job ID = 14167186 SRX = SRX9090277 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18469203 spots for SRR12606610/SRR12606610.sra Written 18469203 spots for SRR12606610/SRR12606610.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167717 ("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: 00:05:55 18469203 reads; of these: 18469203 (100.00%) were unpaired; of these: 523022 (2.83%) aligned 0 times 13450996 (72.83%) aligned exactly 1 time 4495185 (24.34%) aligned >1 times 97.17% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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 8 files... [bam_rmdupse_core] 5641123 / 17946181 = 0.3143 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 11:00:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.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 11:00:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:00:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:00:54: 1000000 INFO @ Fri, 10 Dec 2021 11:01:00: 2000000 INFO @ Fri, 10 Dec 2021 11:01:05: 3000000 INFO @ Fri, 10 Dec 2021 11:01:11: 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 11:01:17: 5000000 INFO @ Fri, 10 Dec 2021 11:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.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 11:01:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:01:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:01:22: 6000000 INFO @ Fri, 10 Dec 2021 11:01:23: 1000000 INFO @ Fri, 10 Dec 2021 11:01:28: 7000000 INFO @ Fri, 10 Dec 2021 11:01:29: 2000000 INFO @ Fri, 10 Dec 2021 11:01:34: 8000000 INFO @ Fri, 10 Dec 2021 11:01:35: 3000000 INFO @ Fri, 10 Dec 2021 11:01:40: 9000000 INFO @ Fri, 10 Dec 2021 11:01:41: 4000000 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 11:01:46: 10000000 INFO @ Fri, 10 Dec 2021 11:01:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.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 11:01:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:01:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:01:48: 5000000 INFO @ Fri, 10 Dec 2021 11:01:52: 11000000 INFO @ Fri, 10 Dec 2021 11:01:54: 1000000 INFO @ Fri, 10 Dec 2021 11:01:55: 6000000 INFO @ Fri, 10 Dec 2021 11:01:58: 12000000 INFO @ Fri, 10 Dec 2021 11:02:00: #1 tag size is determined as 49 bps INFO @ Fri, 10 Dec 2021 11:02:00: #1 tag size = 49 INFO @ Fri, 10 Dec 2021 11:02:00: #1 total tags in treatment: 12305058 INFO @ Fri, 10 Dec 2021 11:02:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:00: #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 11:02:00: #1 tags after filtering in treatment: 12305058 INFO @ Fri, 10 Dec 2021 11:02:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:02:00: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:01: #2 number of paired peaks: 5496 INFO @ Fri, 10 Dec 2021 11:02:01: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:01: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:01: 2000000 INFO @ Fri, 10 Dec 2021 11:02:01: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:01: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:01: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 11:02:01: #2 alternative fragment length(s) may be 3,71 bps INFO @ Fri, 10 Dec 2021 11:02:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.05_model.r WARNING @ Fri, 10 Dec 2021 11:02:01: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:01: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Fri, 10 Dec 2021 11:02:01: #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 11:02:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:02:02: 7000000 INFO @ Fri, 10 Dec 2021 11:02:09: 8000000 INFO @ Fri, 10 Dec 2021 11:02:09: 3000000 INFO @ Fri, 10 Dec 2021 11:02:16: 9000000 INFO @ Fri, 10 Dec 2021 11:02:17: 4000000 INFO @ Fri, 10 Dec 2021 11:02:23: 10000000 INFO @ Fri, 10 Dec 2021 11:02:25: 5000000 INFO @ Fri, 10 Dec 2021 11:02:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:02:30: 11000000 INFO @ Fri, 10 Dec 2021 11:02:33: 6000000 INFO @ Fri, 10 Dec 2021 11:02:36: 12000000 INFO @ Fri, 10 Dec 2021 11:02:39: #1 tag size is determined as 49 bps INFO @ Fri, 10 Dec 2021 11:02:39: #1 tag size = 49 INFO @ Fri, 10 Dec 2021 11:02:39: #1 total tags in treatment: 12305058 INFO @ Fri, 10 Dec 2021 11:02:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:39: #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 11:02:39: #1 tags after filtering in treatment: 12305058 INFO @ Fri, 10 Dec 2021 11:02:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:02:39: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:40: #2 number of paired peaks: 5496 INFO @ Fri, 10 Dec 2021 11:02:40: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:40: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:40: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:40: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:40: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 11:02:40: #2 alternative fragment length(s) may be 3,71 bps INFO @ Fri, 10 Dec 2021 11:02:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.10_model.r WARNING @ Fri, 10 Dec 2021 11:02:40: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:40: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Fri, 10 Dec 2021 11:02:40: #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 11:02:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:02:42: 7000000 INFO @ Fri, 10 Dec 2021 11:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.05_summits.bed INFO @ Fri, 10 Dec 2021 11:02:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7172 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:02:49: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:02:57: 9000000 INFO @ Fri, 10 Dec 2021 11:03:05: 10000000 INFO @ Fri, 10 Dec 2021 11:03:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:03:12: 11000000 INFO @ Fri, 10 Dec 2021 11:03:20: 12000000 INFO @ Fri, 10 Dec 2021 11:03:23: #1 tag size is determined as 49 bps INFO @ Fri, 10 Dec 2021 11:03:23: #1 tag size = 49 INFO @ Fri, 10 Dec 2021 11:03:23: #1 total tags in treatment: 12305058 INFO @ Fri, 10 Dec 2021 11:03:23: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:03:23: #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 11:03:23: #1 tags after filtering in treatment: 12305058 INFO @ Fri, 10 Dec 2021 11:03:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:03:23: #1 finished! INFO @ Fri, 10 Dec 2021 11:03:23: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:03:23: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:03:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:03:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:03:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.10_summits.bed INFO @ Fri, 10 Dec 2021 11:03:24: Done! INFO @ Fri, 10 Dec 2021 11:03:24: #2 number of paired peaks: 5496 INFO @ Fri, 10 Dec 2021 11:03:24: start model_add_line... INFO @ Fri, 10 Dec 2021 11:03:24: start X-correlation... INFO @ Fri, 10 Dec 2021 11:03:24: end of X-cor INFO @ Fri, 10 Dec 2021 11:03:24: #2 finished! INFO @ Fri, 10 Dec 2021 11:03:24: #2 predicted fragment length is 71 bps INFO @ Fri, 10 Dec 2021 11:03:24: #2 alternative fragment length(s) may be 3,71 bps INFO @ Fri, 10 Dec 2021 11:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.20_model.r WARNING @ Fri, 10 Dec 2021 11:03:24: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:03:24: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Fri, 10 Dec 2021 11:03:24: #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 11:03:24: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:03:24: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 7 millis pass2 - checking and writing primary data (3923 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:03:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:04:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:04:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:04:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9090277/SRX9090277.20_summits.bed INFO @ Fri, 10 Dec 2021 11:04:07: Done! pass1 - making usageList (13 chroms): 8 millis pass2 - checking and writing primary data (1742 records, 4 fields): 7 millis CompletedMACS2peakCalling