Job ID = 14166966 SRX = SRX7723704 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32667414 spots for SRR11084660/SRR11084660.sra Written 32667414 spots for SRR11084660/SRR11084660.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167302 ("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: 00:13:10 32667414 reads; of these: 32667414 (100.00%) were unpaired; of these: 8270831 (25.32%) aligned 0 times 15028535 (46.00%) aligned exactly 1 time 9368048 (28.68%) aligned >1 times 74.68% overall alignment rate Time searching: 00:13:10 Overall time: 00:13:10 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] 8000752 / 24396583 = 0.3279 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 08:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.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 08:31:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:31:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:31:34: 1000000 INFO @ Fri, 10 Dec 2021 08:31:40: 2000000 INFO @ Fri, 10 Dec 2021 08:31:47: 3000000 INFO @ Fri, 10 Dec 2021 08:31:53: 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 08:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.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 08:31:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:31:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:32:00: 5000000 INFO @ Fri, 10 Dec 2021 08:32:05: 1000000 INFO @ Fri, 10 Dec 2021 08:32:07: 6000000 INFO @ Fri, 10 Dec 2021 08:32:12: 2000000 INFO @ Fri, 10 Dec 2021 08:32:14: 7000000 INFO @ Fri, 10 Dec 2021 08:32:20: 3000000 INFO @ Fri, 10 Dec 2021 08:32:22: 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 08:32:27: 4000000 INFO @ Fri, 10 Dec 2021 08:32:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.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 08:32:27: #1 read tag files... INFO @ Fri, 10 Dec 2021 08:32:27: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 08:32:29: 9000000 INFO @ Fri, 10 Dec 2021 08:32:35: 5000000 INFO @ Fri, 10 Dec 2021 08:32:35: 1000000 INFO @ Fri, 10 Dec 2021 08:32:36: 10000000 INFO @ Fri, 10 Dec 2021 08:32:42: 2000000 INFO @ Fri, 10 Dec 2021 08:32:42: 6000000 INFO @ Fri, 10 Dec 2021 08:32:44: 11000000 INFO @ Fri, 10 Dec 2021 08:32:50: 3000000 INFO @ Fri, 10 Dec 2021 08:32:50: 7000000 INFO @ Fri, 10 Dec 2021 08:32:51: 12000000 INFO @ Fri, 10 Dec 2021 08:32:57: 4000000 INFO @ Fri, 10 Dec 2021 08:32:57: 8000000 INFO @ Fri, 10 Dec 2021 08:32:59: 13000000 INFO @ Fri, 10 Dec 2021 08:33:05: 5000000 INFO @ Fri, 10 Dec 2021 08:33:05: 9000000 INFO @ Fri, 10 Dec 2021 08:33:06: 14000000 INFO @ Fri, 10 Dec 2021 08:33:12: 6000000 INFO @ Fri, 10 Dec 2021 08:33:13: 10000000 INFO @ Fri, 10 Dec 2021 08:33:13: 15000000 INFO @ Fri, 10 Dec 2021 08:33:19: 7000000 INFO @ Fri, 10 Dec 2021 08:33:20: 11000000 INFO @ Fri, 10 Dec 2021 08:33:21: 16000000 INFO @ Fri, 10 Dec 2021 08:33:24: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:33:24: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:33:24: #1 total tags in treatment: 16395831 INFO @ Fri, 10 Dec 2021 08:33:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:33:24: #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 08:33:24: #1 tags after filtering in treatment: 16395831 INFO @ Fri, 10 Dec 2021 08:33:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:33:24: #1 finished! INFO @ Fri, 10 Dec 2021 08:33:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:33:25: #2 number of paired peaks: 2903 INFO @ Fri, 10 Dec 2021 08:33:25: start model_add_line... INFO @ Fri, 10 Dec 2021 08:33:25: start X-correlation... INFO @ Fri, 10 Dec 2021 08:33:25: end of X-cor INFO @ Fri, 10 Dec 2021 08:33:25: #2 finished! INFO @ Fri, 10 Dec 2021 08:33:25: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 08:33:25: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 10 Dec 2021 08:33:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.05_model.r WARNING @ Fri, 10 Dec 2021 08:33:26: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:33:26: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Fri, 10 Dec 2021 08:33:26: #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 08:33:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:33:27: 8000000 INFO @ Fri, 10 Dec 2021 08:33:28: 12000000 INFO @ Fri, 10 Dec 2021 08:33:34: 9000000 INFO @ Fri, 10 Dec 2021 08:33:35: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 08:33:41: 10000000 INFO @ Fri, 10 Dec 2021 08:33:42: 14000000 INFO @ Fri, 10 Dec 2021 08:33:48: 11000000 INFO @ Fri, 10 Dec 2021 08:33:50: 15000000 INFO @ Fri, 10 Dec 2021 08:33:56: 12000000 INFO @ Fri, 10 Dec 2021 08:33:57: 16000000 INFO @ Fri, 10 Dec 2021 08:34:00: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:34:00: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:34:00: #1 total tags in treatment: 16395831 INFO @ Fri, 10 Dec 2021 08:34:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:34:00: #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 08:34:00: #1 tags after filtering in treatment: 16395831 INFO @ Fri, 10 Dec 2021 08:34:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:34:00: #1 finished! INFO @ Fri, 10 Dec 2021 08:34:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:34:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:34:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:34:01: #2 number of paired peaks: 2903 INFO @ Fri, 10 Dec 2021 08:34:01: start model_add_line... INFO @ Fri, 10 Dec 2021 08:34:02: start X-correlation... INFO @ Fri, 10 Dec 2021 08:34:02: end of X-cor INFO @ Fri, 10 Dec 2021 08:34:02: #2 finished! INFO @ Fri, 10 Dec 2021 08:34:02: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 08:34:02: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 10 Dec 2021 08:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.10_model.r WARNING @ Fri, 10 Dec 2021 08:34:02: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:34:02: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Fri, 10 Dec 2021 08:34:02: #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 08:34:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:34:03: 13000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 08:34:10: 14000000 INFO @ Fri, 10 Dec 2021 08:34:16: 15000000 INFO @ Fri, 10 Dec 2021 08:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.05_peaks.xls INFO @ Fri, 10 Dec 2021 08:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.05_summits.bed INFO @ Fri, 10 Dec 2021 08:34:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (17519 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:34:23: 16000000 INFO @ Fri, 10 Dec 2021 08:34:25: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 08:34:25: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 08:34:25: #1 total tags in treatment: 16395831 INFO @ Fri, 10 Dec 2021 08:34:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 08:34:25: #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 08:34:25: #1 tags after filtering in treatment: 16395831 INFO @ Fri, 10 Dec 2021 08:34:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 08:34:25: #1 finished! INFO @ Fri, 10 Dec 2021 08:34:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 08:34:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 08:34:27: #2 number of paired peaks: 2903 INFO @ Fri, 10 Dec 2021 08:34:27: start model_add_line... INFO @ Fri, 10 Dec 2021 08:34:27: start X-correlation... INFO @ Fri, 10 Dec 2021 08:34:27: end of X-cor INFO @ Fri, 10 Dec 2021 08:34:27: #2 finished! INFO @ Fri, 10 Dec 2021 08:34:27: #2 predicted fragment length is 110 bps INFO @ Fri, 10 Dec 2021 08:34:27: #2 alternative fragment length(s) may be 110 bps INFO @ Fri, 10 Dec 2021 08:34:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.20_model.r WARNING @ Fri, 10 Dec 2021 08:34:27: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 08:34:27: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Fri, 10 Dec 2021 08:34:27: #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 08:34:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 08:34:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 08:34:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:34:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.10_peaks.xls INFO @ Fri, 10 Dec 2021 08:34:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:34:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.10_summits.bed INFO @ Fri, 10 Dec 2021 08:34:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9766 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 08:35:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 08:35:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.20_peaks.xls INFO @ Fri, 10 Dec 2021 08:35:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 08:35:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723704/SRX7723704.20_summits.bed INFO @ Fri, 10 Dec 2021 08:35:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4597 records, 4 fields): 6 millis CompletedMACS2peakCalling