Job ID = 10166164 SRX = SRX7723702 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34021743 spots for SRR11084658/SRR11084658.sra Written 34021743 spots for SRR11084658/SRR11084658.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166567 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:35 34021743 reads; of these: 34021743 (100.00%) were unpaired; of these: 15225434 (44.75%) aligned 0 times 14749686 (43.35%) aligned exactly 1 time 4046623 (11.89%) aligned >1 times 55.25% overall alignment rate Time searching: 00:10:36 Overall time: 00:10:36 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] 9533957 / 18796309 = 0.5072 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 20:51:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.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 20:51:39: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:51:39: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:51:47: 1000000 INFO @ Thu, 08 Oct 2020 20:51:55: 2000000 INFO @ Thu, 08 Oct 2020 20:52:02: 3000000 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 20:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.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 20:52:09: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:52:09: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:52:10: 4000000 INFO @ Thu, 08 Oct 2020 20:52:17: 1000000 INFO @ Thu, 08 Oct 2020 20:52:19: 5000000 INFO @ Thu, 08 Oct 2020 20:52:25: 2000000 INFO @ Thu, 08 Oct 2020 20:52:28: 6000000 INFO @ Thu, 08 Oct 2020 20:52:34: 3000000 INFO @ Thu, 08 Oct 2020 20:52:36: 7000000 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 20:52:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.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 20:52:42: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:52:42: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:52:42: 4000000 INFO @ Thu, 08 Oct 2020 20:52:45: 8000000 INFO @ Thu, 08 Oct 2020 20:52:50: 1000000 INFO @ Thu, 08 Oct 2020 20:52:51: 5000000 INFO @ Thu, 08 Oct 2020 20:52:54: 9000000 INFO @ Thu, 08 Oct 2020 20:52:56: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:52:56: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:52:56: #1 total tags in treatment: 9262352 INFO @ Thu, 08 Oct 2020 20:52:56: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:52:56: #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 20:52:56: #1 tags after filtering in treatment: 9262352 INFO @ Thu, 08 Oct 2020 20:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:52:56: #1 finished! INFO @ Thu, 08 Oct 2020 20:52:56: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:52:57: #2 number of paired peaks: 6693 INFO @ Thu, 08 Oct 2020 20:52:57: start model_add_line... INFO @ Thu, 08 Oct 2020 20:52:57: start X-correlation... INFO @ Thu, 08 Oct 2020 20:52:57: end of X-cor INFO @ Thu, 08 Oct 2020 20:52:57: #2 finished! INFO @ Thu, 08 Oct 2020 20:52:57: #2 predicted fragment length is 132 bps INFO @ Thu, 08 Oct 2020 20:52:57: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 08 Oct 2020 20:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05_model.r WARNING @ Thu, 08 Oct 2020 20:52:57: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:52:57: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 08 Oct 2020 20:52:57: #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 20:52:57: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:52:59: 2000000 INFO @ Thu, 08 Oct 2020 20:52:59: 6000000 INFO @ Thu, 08 Oct 2020 20:53:06: 3000000 INFO @ Thu, 08 Oct 2020 20:53:07: 7000000 INFO @ Thu, 08 Oct 2020 20:53:14: 4000000 INFO @ Thu, 08 Oct 2020 20:53:15: 8000000 INFO @ Thu, 08 Oct 2020 20:53:19: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:53:22: 5000000 INFO @ Thu, 08 Oct 2020 20:53:22: 9000000 INFO @ Thu, 08 Oct 2020 20:53:24: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:53:24: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:53:24: #1 total tags in treatment: 9262352 INFO @ Thu, 08 Oct 2020 20:53:24: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:53:24: #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 20:53:25: #1 tags after filtering in treatment: 9262352 INFO @ Thu, 08 Oct 2020 20:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:53:25: #1 finished! INFO @ Thu, 08 Oct 2020 20:53:25: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:53:26: #2 number of paired peaks: 6693 INFO @ Thu, 08 Oct 2020 20:53:26: start model_add_line... INFO @ Thu, 08 Oct 2020 20:53:26: start X-correlation... INFO @ Thu, 08 Oct 2020 20:53:26: end of X-cor INFO @ Thu, 08 Oct 2020 20:53:26: #2 finished! INFO @ Thu, 08 Oct 2020 20:53:26: #2 predicted fragment length is 132 bps INFO @ Thu, 08 Oct 2020 20:53:26: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 08 Oct 2020 20:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10_model.r WARNING @ Thu, 08 Oct 2020 20:53:26: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:53:26: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 08 Oct 2020 20:53:26: #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 20:53:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:53:29: 6000000 INFO @ Thu, 08 Oct 2020 20:53:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:53:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.05_summits.bed INFO @ Thu, 08 Oct 2020 20:53:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9514 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:53:37: 7000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:53:44: 8000000 INFO @ Thu, 08 Oct 2020 20:53:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:53:51: 9000000 INFO @ Thu, 08 Oct 2020 20:53:53: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 20:53:53: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 20:53:53: #1 total tags in treatment: 9262352 INFO @ Thu, 08 Oct 2020 20:53:53: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:53:53: #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 20:53:53: #1 tags after filtering in treatment: 9262352 INFO @ Thu, 08 Oct 2020 20:53:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:53:53: #1 finished! INFO @ Thu, 08 Oct 2020 20:53:53: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:53:54: #2 number of paired peaks: 6693 INFO @ Thu, 08 Oct 2020 20:53:54: start model_add_line... INFO @ Thu, 08 Oct 2020 20:53:55: start X-correlation... INFO @ Thu, 08 Oct 2020 20:53:55: end of X-cor INFO @ Thu, 08 Oct 2020 20:53:55: #2 finished! INFO @ Thu, 08 Oct 2020 20:53:55: #2 predicted fragment length is 132 bps INFO @ Thu, 08 Oct 2020 20:53:55: #2 alternative fragment length(s) may be 132 bps INFO @ Thu, 08 Oct 2020 20:53:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20_model.r WARNING @ Thu, 08 Oct 2020 20:53:55: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:53:55: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Thu, 08 Oct 2020 20:53:55: #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 20:53:55: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:53:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:53:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:53:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:53:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.10_summits.bed INFO @ Thu, 08 Oct 2020 20:53:59: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6992 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:54:16: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:54:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:54:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:54:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723702/SRX7723702.20_summits.bed INFO @ Thu, 08 Oct 2020 20:54:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4414 records, 4 fields): 6 millis CompletedMACS2peakCalling