Job ID = 14166970 SRX = SRX7723708 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28127043 spots for SRR11084664/SRR11084664.sra Written 28127043 spots for SRR11084664/SRR11084664.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167313 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:30 28127043 reads; of these: 28127043 (100.00%) were unpaired; of these: 6222548 (22.12%) aligned 0 times 13934464 (49.54%) aligned exactly 1 time 7970031 (28.34%) aligned >1 times 77.88% overall alignment rate Time searching: 00:14:31 Overall time: 00:14:31 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] 6930059 / 21904495 = 0.3164 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 08:39:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.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 08:39:14: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:39:14: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:39:26: 1000000 INFO @ Fri, 10 Dec 2021 08:39:38: 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 @ Fri, 10 Dec 2021 08:39:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.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 08:39:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:39:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:39:50: 3000000 INFO @ Fri, 10 Dec 2021 08:39:52: 1000000 INFO @ Fri, 10 Dec 2021 08:40:01: 2000000 INFO @ Fri, 10 Dec 2021 08:40:03: 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 08:40:10: 3000000 INFO @ Fri, 10 Dec 2021 08:40:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.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 08:40:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:40:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:40:15: 5000000 INFO @ Fri, 10 Dec 2021 08:40:20: 4000000 INFO @ Fri, 10 Dec 2021 08:40:23: 1000000 INFO @ Fri, 10 Dec 2021 08:40:27: 6000000 INFO @ Fri, 10 Dec 2021 08:40:29: 5000000 INFO @ Fri, 10 Dec 2021 08:40:33: 2000000 INFO @ Fri, 10 Dec 2021 08:40:38: 6000000 INFO @ Fri, 10 Dec 2021 08:40:40: 7000000 INFO @ Fri, 10 Dec 2021 08:40:43: 3000000 INFO @ Fri, 10 Dec 2021 08:40:47: 7000000 INFO @ Fri, 10 Dec 2021 08:40:53: 8000000 INFO @ Fri, 10 Dec 2021 08:40:53: 4000000 INFO @ Fri, 10 Dec 2021 08:40:57: 8000000 INFO @ Fri, 10 Dec 2021 08:41:03: 5000000 INFO @ Fri, 10 Dec 2021 08:41:05: 9000000 INFO @ Fri, 10 Dec 2021 08:41:06: 9000000 INFO @ Fri, 10 Dec 2021 08:41:14: 6000000 INFO @ Fri, 10 Dec 2021 08:41:16: 10000000 INFO @ Fri, 10 Dec 2021 08:41:18: 10000000 INFO @ Fri, 10 Dec 2021 08:41:24: 7000000 INFO @ Fri, 10 Dec 2021 08:41:25: 11000000 INFO @ Fri, 10 Dec 2021 08:41:31: 11000000 INFO @ Fri, 10 Dec 2021 08:41:34: 8000000 INFO @ Fri, 10 Dec 2021 08:41:34: 12000000 INFO @ Fri, 10 Dec 2021 08:41:43: 12000000 INFO @ Fri, 10 Dec 2021 08:41:44: 13000000 INFO @ Fri, 10 Dec 2021 08:41:45: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:41:53: 14000000 INFO @ Fri, 10 Dec 2021 08:41:55: 10000000 INFO @ Fri, 10 Dec 2021 08:41:55: 13000000 INFO @ Fri, 10 Dec 2021 08:42:02: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:42:02: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:42:02: #1 total tags in treatment: 14974436 INFO @ Fri, 10 Dec 2021 08:42:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:42:02: #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 08:42:02: #1 tags after filtering in treatment: 14974436 INFO @ Fri, 10 Dec 2021 08:42:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:42:02: #1 finished! INFO @ Fri, 10 Dec 2021 08:42:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:42:04: #2 number of paired peaks: 2519 INFO @ Fri, 10 Dec 2021 08:42:04: start model_add_line... INFO @ Fri, 10 Dec 2021 08:42:04: start X-correlation... INFO @ Fri, 10 Dec 2021 08:42:04: end of X-cor INFO @ Fri, 10 Dec 2021 08:42:04: #2 finished! INFO @ Fri, 10 Dec 2021 08:42:04: #2 predicted fragment length is 101 bps INFO @ Fri, 10 Dec 2021 08:42:04: #2 alternative fragment length(s) may be 101 bps INFO @ Fri, 10 Dec 2021 08:42:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10_model.r WARNING @ Fri, 10 Dec 2021 08:42:04: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:42:04: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Fri, 10 Dec 2021 08:42:04: #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 08:42:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:42:05: 11000000 INFO @ Fri, 10 Dec 2021 08:42:08: 14000000 INFO @ Fri, 10 Dec 2021 08:42:15: 12000000 INFO @ Fri, 10 Dec 2021 08:42:19: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:42:19: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:42:19: #1 total tags in treatment: 14974436 INFO @ Fri, 10 Dec 2021 08:42:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:42:19: #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 08:42:20: #1 tags after filtering in treatment: 14974436 INFO @ Fri, 10 Dec 2021 08:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:42:20: #1 finished! INFO @ Fri, 10 Dec 2021 08:42:20: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:42:21: #2 number of paired peaks: 2519 INFO @ Fri, 10 Dec 2021 08:42:21: start model_add_line... INFO @ Fri, 10 Dec 2021 08:42:21: start X-correlation... INFO @ Fri, 10 Dec 2021 08:42:21: end of X-cor INFO @ Fri, 10 Dec 2021 08:42:21: #2 finished! INFO @ Fri, 10 Dec 2021 08:42:21: #2 predicted fragment length is 101 bps INFO @ Fri, 10 Dec 2021 08:42:21: #2 alternative fragment length(s) may be 101 bps INFO @ Fri, 10 Dec 2021 08:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05_model.r WARNING @ Fri, 10 Dec 2021 08:42:21: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:42:21: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Fri, 10 Dec 2021 08:42:21: #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 08:42:21: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:42:25: 13000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:42:34: 14000000 INFO @ Fri, 10 Dec 2021 08:42:44: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:42:44: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:42:44: #1 total tags in treatment: 14974436 INFO @ Fri, 10 Dec 2021 08:42:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:42:44: #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 08:42:44: #1 tags after filtering in treatment: 14974436 INFO @ Fri, 10 Dec 2021 08:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:42:44: #1 finished! INFO @ Fri, 10 Dec 2021 08:42:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:42:46: #2 number of paired peaks: 2519 INFO @ Fri, 10 Dec 2021 08:42:46: start model_add_line... INFO @ Fri, 10 Dec 2021 08:42:46: start X-correlation... INFO @ Fri, 10 Dec 2021 08:42:46: end of X-cor INFO @ Fri, 10 Dec 2021 08:42:46: #2 finished! INFO @ Fri, 10 Dec 2021 08:42:46: #2 predicted fragment length is 101 bps INFO @ Fri, 10 Dec 2021 08:42:46: #2 alternative fragment length(s) may be 101 bps INFO @ Fri, 10 Dec 2021 08:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20_model.r WARNING @ Fri, 10 Dec 2021 08:42:46: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:42:46: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Fri, 10 Dec 2021 08:42:46: #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 08:42:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:42:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:43:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:43:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:43:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:43:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10_summits.bed INFO @ Fri, 10 Dec 2021 08:43:09: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8789 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:43:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:43:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:43:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05_summits.bed INFO @ Fri, 10 Dec 2021 08:43:26: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (16392 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:43:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:43:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:43:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:43:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20_summits.bed INFO @ Fri, 10 Dec 2021 08:43:49: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (3964 records, 4 fields): 13 millis CompletedMACS2peakCalling