Job ID = 14172054 SRX = SRX10089755 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30454379 spots for SRR13700642/SRR13700642.sra Written 30454379 spots for SRR13700642/SRR13700642.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172515 ("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: 00:05:43 30454379 reads; of these: 30454379 (100.00%) were unpaired; of these: 26403918 (86.70%) aligned 0 times 3441896 (11.30%) aligned exactly 1 time 608565 (2.00%) aligned >1 times 13.30% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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_rmdupse_core] 528995 / 4050461 = 0.1306 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 14:03:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.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 14:03:29: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:03:29: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:03:40: 1000000 INFO @ Sat, 11 Dec 2021 14:03:51: 2000000 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 14:03:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.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 14:03:59: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:03:59: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:04:02: 3000000 INFO @ Sat, 11 Dec 2021 14:04:08: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 14:04:08: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 14:04:08: #1 total tags in treatment: 3521466 INFO @ Sat, 11 Dec 2021 14:04:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:04:08: #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 14:04:08: #1 tags after filtering in treatment: 3521466 INFO @ Sat, 11 Dec 2021 14:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:04:08: #1 finished! INFO @ Sat, 11 Dec 2021 14:04:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:04:08: #2 number of paired peaks: 2847 INFO @ Sat, 11 Dec 2021 14:04:08: start model_add_line... INFO @ Sat, 11 Dec 2021 14:04:09: start X-correlation... INFO @ Sat, 11 Dec 2021 14:04:09: end of X-cor INFO @ Sat, 11 Dec 2021 14:04:09: #2 finished! INFO @ Sat, 11 Dec 2021 14:04:09: #2 predicted fragment length is 138 bps INFO @ Sat, 11 Dec 2021 14:04:09: #2 alternative fragment length(s) may be 138 bps INFO @ Sat, 11 Dec 2021 14:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.05_model.r WARNING @ Sat, 11 Dec 2021 14:04:09: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:04:09: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Sat, 11 Dec 2021 14:04:09: #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 14:04:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:04:09: 1000000 INFO @ Sat, 11 Dec 2021 14:04:19: 2000000 INFO @ Sat, 11 Dec 2021 14:04:21: #3 Call peaks for each chromosome... 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 14:04:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:04:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:04:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.05_summits.bed INFO @ Sat, 11 Dec 2021 14:04:28: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4556 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.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 14:04:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:04:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:04:29: 3000000 INFO @ Sat, 11 Dec 2021 14:04:34: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 14:04:34: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 14:04:34: #1 total tags in treatment: 3521466 INFO @ Sat, 11 Dec 2021 14:04:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:04:34: #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 14:04:34: #1 tags after filtering in treatment: 3521466 INFO @ Sat, 11 Dec 2021 14:04:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:04:34: #1 finished! INFO @ Sat, 11 Dec 2021 14:04:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:04:34: #2 number of paired peaks: 2847 INFO @ Sat, 11 Dec 2021 14:04:34: start model_add_line... INFO @ Sat, 11 Dec 2021 14:04:34: start X-correlation... INFO @ Sat, 11 Dec 2021 14:04:34: end of X-cor INFO @ Sat, 11 Dec 2021 14:04:34: #2 finished! INFO @ Sat, 11 Dec 2021 14:04:34: #2 predicted fragment length is 138 bps INFO @ Sat, 11 Dec 2021 14:04:34: #2 alternative fragment length(s) may be 138 bps INFO @ Sat, 11 Dec 2021 14:04:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.10_model.r WARNING @ Sat, 11 Dec 2021 14:04:34: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:04:34: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Sat, 11 Dec 2021 14:04:34: #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 14:04:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:04:41: 1000000 INFO @ Sat, 11 Dec 2021 14:04:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:04:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:04:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:04:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.10_summits.bed INFO @ Sat, 11 Dec 2021 14:04:53: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2487 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:04:53: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:05:06: 3000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:05:12: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 14:05:12: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 14:05:12: #1 total tags in treatment: 3521466 INFO @ Sat, 11 Dec 2021 14:05:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:05:12: #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 14:05:12: #1 tags after filtering in treatment: 3521466 INFO @ Sat, 11 Dec 2021 14:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:05:12: #1 finished! INFO @ Sat, 11 Dec 2021 14:05:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:05:13: #2 number of paired peaks: 2847 INFO @ Sat, 11 Dec 2021 14:05:13: start model_add_line... INFO @ Sat, 11 Dec 2021 14:05:13: start X-correlation... INFO @ Sat, 11 Dec 2021 14:05:13: end of X-cor INFO @ Sat, 11 Dec 2021 14:05:13: #2 finished! INFO @ Sat, 11 Dec 2021 14:05:13: #2 predicted fragment length is 138 bps INFO @ Sat, 11 Dec 2021 14:05:13: #2 alternative fragment length(s) may be 138 bps INFO @ Sat, 11 Dec 2021 14:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.20_model.r WARNING @ Sat, 11 Dec 2021 14:05:13: #2 Since the d (138) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:05:13: #2 You may need to consider one of the other alternative d(s): 138 WARNING @ Sat, 11 Dec 2021 14:05:13: #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 14:05:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:05:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:05:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:05:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:05:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089755/SRX10089755.20_summits.bed INFO @ Sat, 11 Dec 2021 14:05:30: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1119 records, 4 fields): 6 millis CompletedMACS2peakCalling