Job ID = 10166186 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 10166589 ("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: 00:11:20 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: 00:11:20 Overall time: 00:11:20 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:54:21: # 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 @ Thu, 08 Oct 2020 20:54:21: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:54:21: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:54:27: 1000000 INFO @ Thu, 08 Oct 2020 20:54:33: 2000000 INFO @ Thu, 08 Oct 2020 20:54:39: 3000000 INFO @ Thu, 08 Oct 2020 20:54:44: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:54:50: 5000000 INFO @ Thu, 08 Oct 2020 20:54:51: # 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 @ Thu, 08 Oct 2020 20:54:51: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:54:51: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:54:56: 6000000 INFO @ Thu, 08 Oct 2020 20:54:58: 1000000 INFO @ Thu, 08 Oct 2020 20:55:02: 7000000 INFO @ Thu, 08 Oct 2020 20:55:04: 2000000 INFO @ Thu, 08 Oct 2020 20:55:08: 8000000 INFO @ Thu, 08 Oct 2020 20:55:10: 3000000 INFO @ Thu, 08 Oct 2020 20:55:14: 9000000 INFO @ Thu, 08 Oct 2020 20:55:16: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:55:20: 10000000 INFO @ Thu, 08 Oct 2020 20:55:21: # 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 @ Thu, 08 Oct 2020 20:55:21: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:55:21: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:55:22: 5000000 INFO @ Thu, 08 Oct 2020 20:55:26: 11000000 INFO @ Thu, 08 Oct 2020 20:55:28: 1000000 INFO @ Thu, 08 Oct 2020 20:55:29: 6000000 INFO @ Thu, 08 Oct 2020 20:55:32: 12000000 INFO @ Thu, 08 Oct 2020 20:55:35: 2000000 INFO @ Thu, 08 Oct 2020 20:55:35: 7000000 INFO @ Thu, 08 Oct 2020 20:55:39: 13000000 INFO @ Thu, 08 Oct 2020 20:55:41: 3000000 INFO @ Thu, 08 Oct 2020 20:55:41: 8000000 INFO @ Thu, 08 Oct 2020 20:55:45: 14000000 INFO @ Thu, 08 Oct 2020 20:55:47: 4000000 INFO @ Thu, 08 Oct 2020 20:55:48: 9000000 INFO @ Thu, 08 Oct 2020 20:55:51: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:55:51: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:55:51: #1 total tags in treatment: 14974436 INFO @ Thu, 08 Oct 2020 20:55:51: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:55:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:55:51: #1 tags after filtering in treatment: 14974436 INFO @ Thu, 08 Oct 2020 20:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:55:51: #1 finished! INFO @ Thu, 08 Oct 2020 20:55:51: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:55:53: #2 number of paired peaks: 2519 INFO @ Thu, 08 Oct 2020 20:55:53: start model_add_line... INFO @ Thu, 08 Oct 2020 20:55:53: start X-correlation... INFO @ Thu, 08 Oct 2020 20:55:53: end of X-cor INFO @ Thu, 08 Oct 2020 20:55:53: #2 finished! INFO @ Thu, 08 Oct 2020 20:55:53: #2 predicted fragment length is 101 bps INFO @ Thu, 08 Oct 2020 20:55:53: #2 alternative fragment length(s) may be 101 bps INFO @ Thu, 08 Oct 2020 20:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05_model.r WARNING @ Thu, 08 Oct 2020 20:55:53: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:55:53: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Thu, 08 Oct 2020 20:55:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:55:53: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:55:54: 5000000 INFO @ Thu, 08 Oct 2020 20:55:54: 10000000 INFO @ Thu, 08 Oct 2020 20:56:00: 6000000 INFO @ Thu, 08 Oct 2020 20:56:00: 11000000 INFO @ Thu, 08 Oct 2020 20:56:06: 12000000 INFO @ Thu, 08 Oct 2020 20:56:06: 7000000 INFO @ Thu, 08 Oct 2020 20:56:12: 13000000 INFO @ Thu, 08 Oct 2020 20:56:12: 8000000 INFO @ Thu, 08 Oct 2020 20:56:19: 9000000 INFO @ Thu, 08 Oct 2020 20:56:19: 14000000 INFO @ Thu, 08 Oct 2020 20:56:24: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:56:25: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:56:25: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:56:25: #1 total tags in treatment: 14974436 INFO @ Thu, 08 Oct 2020 20:56:25: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:56:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:56:25: 10000000 INFO @ Thu, 08 Oct 2020 20:56:25: #1 tags after filtering in treatment: 14974436 INFO @ Thu, 08 Oct 2020 20:56:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:56:25: #1 finished! INFO @ Thu, 08 Oct 2020 20:56:25: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:56:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:56:26: #2 number of paired peaks: 2519 INFO @ Thu, 08 Oct 2020 20:56:26: start model_add_line... INFO @ Thu, 08 Oct 2020 20:56:26: start X-correlation... INFO @ Thu, 08 Oct 2020 20:56:26: end of X-cor INFO @ Thu, 08 Oct 2020 20:56:26: #2 finished! INFO @ Thu, 08 Oct 2020 20:56:26: #2 predicted fragment length is 101 bps INFO @ Thu, 08 Oct 2020 20:56:26: #2 alternative fragment length(s) may be 101 bps INFO @ Thu, 08 Oct 2020 20:56:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10_model.r WARNING @ Thu, 08 Oct 2020 20:56:26: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:56:26: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Thu, 08 Oct 2020 20:56:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:56:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:56:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:56:31: 11000000 INFO @ Thu, 08 Oct 2020 20:56:36: 12000000 INFO @ Thu, 08 Oct 2020 20:56:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:56:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:56:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.05_summits.bed INFO @ Thu, 08 Oct 2020 20:56:41: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (16392 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:56:42: 13000000 INFO @ Thu, 08 Oct 2020 20:56:48: 14000000 INFO @ Thu, 08 Oct 2020 20:56:54: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:56:54: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:56:54: #1 total tags in treatment: 14974436 INFO @ Thu, 08 Oct 2020 20:56:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:56:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:56:54: #1 tags after filtering in treatment: 14974436 INFO @ Thu, 08 Oct 2020 20:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:56:54: #1 finished! INFO @ Thu, 08 Oct 2020 20:56:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:56:55: #2 number of paired peaks: 2519 INFO @ Thu, 08 Oct 2020 20:56:55: start model_add_line... INFO @ Thu, 08 Oct 2020 20:56:55: start X-correlation... INFO @ Thu, 08 Oct 2020 20:56:55: end of X-cor INFO @ Thu, 08 Oct 2020 20:56:55: #2 finished! INFO @ Thu, 08 Oct 2020 20:56:55: #2 predicted fragment length is 101 bps INFO @ Thu, 08 Oct 2020 20:56:55: #2 alternative fragment length(s) may be 101 bps INFO @ Thu, 08 Oct 2020 20:56:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20_model.r WARNING @ Thu, 08 Oct 2020 20:56:55: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:56:55: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Thu, 08 Oct 2020 20:56:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:56:55: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:56:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:56:59: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.10_summits.bed INFO @ Thu, 08 Oct 2020 20:57:15: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8789 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:57:28: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:57:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:57:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:57:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723708/SRX7723708.20_summits.bed INFO @ Thu, 08 Oct 2020 20:57:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3964 records, 4 fields): 6 millis CompletedMACS2peakCalling