Job ID = 16439991 SRX = SRX12175827 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23907545 spots for SRR15884966/SRR15884966.sra Written 23907545 spots for SRR15884966/SRR15884966.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440232 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:50:12 23907545 reads; of these: 23907545 (100.00%) were paired; of these: 17867726 (74.74%) aligned concordantly 0 times 4778342 (19.99%) aligned concordantly exactly 1 time 1261477 (5.28%) aligned concordantly >1 times ---- 17867726 pairs aligned concordantly 0 times; of these: 1711908 (9.58%) aligned discordantly 1 time ---- 16155818 pairs aligned 0 times concordantly or discordantly; of these: 32311636 mates make up the pairs; of these: 31035443 (96.05%) aligned 0 times 555455 (1.72%) aligned exactly 1 time 720738 (2.23%) aligned >1 times 35.09% overall alignment rate Time searching: 00:50:13 Overall time: 00:50:13 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 993891 / 7711963 = 0.1289 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:37:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.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 @ Tue, 02 Aug 2022 17:37:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:37:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:37:31: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:37:45: 2000000 INFO @ Tue, 02 Aug 2022 17:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.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 @ Tue, 02 Aug 2022 17:37:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:37:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:37:59: 3000000 INFO @ Tue, 02 Aug 2022 17:38:02: 1000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 17:38:14: 4000000 INFO @ Tue, 02 Aug 2022 17:38:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.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 @ Tue, 02 Aug 2022 17:38:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:38:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:38:19: 2000000 INFO @ Tue, 02 Aug 2022 17:38:30: 1000000 INFO @ Tue, 02 Aug 2022 17:38:31: 5000000 INFO @ Tue, 02 Aug 2022 17:38:35: 3000000 INFO @ Tue, 02 Aug 2022 17:38:45: 2000000 INFO @ Tue, 02 Aug 2022 17:38:49: 6000000 INFO @ Tue, 02 Aug 2022 17:38:52: 4000000 INFO @ Tue, 02 Aug 2022 17:39:00: 3000000 INFO @ Tue, 02 Aug 2022 17:39:06: 7000000 INFO @ Tue, 02 Aug 2022 17:39:09: 5000000 INFO @ Tue, 02 Aug 2022 17:39:16: 4000000 INFO @ Tue, 02 Aug 2022 17:39:23: 8000000 INFO @ Tue, 02 Aug 2022 17:39:27: 6000000 INFO @ Tue, 02 Aug 2022 17:39:33: 5000000 INFO @ Tue, 02 Aug 2022 17:39:41: 9000000 INFO @ Tue, 02 Aug 2022 17:39:45: 7000000 INFO @ Tue, 02 Aug 2022 17:39:49: 6000000 INFO @ Tue, 02 Aug 2022 17:40:00: 10000000 INFO @ Tue, 02 Aug 2022 17:40:02: 8000000 INFO @ Tue, 02 Aug 2022 17:40:04: 7000000 INFO @ Tue, 02 Aug 2022 17:40:17: 11000000 INFO @ Tue, 02 Aug 2022 17:40:19: 9000000 INFO @ Tue, 02 Aug 2022 17:40:20: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:40:36: 12000000 INFO @ Tue, 02 Aug 2022 17:40:36: 9000000 INFO @ Tue, 02 Aug 2022 17:40:36: 10000000 INFO @ Tue, 02 Aug 2022 17:40:51: 10000000 INFO @ Tue, 02 Aug 2022 17:40:53: 13000000 INFO @ Tue, 02 Aug 2022 17:40:53: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:41:07: 11000000 INFO @ Tue, 02 Aug 2022 17:41:10: 14000000 INFO @ Tue, 02 Aug 2022 17:41:10: 12000000 INFO @ Tue, 02 Aug 2022 17:41:23: 12000000 INFO @ Tue, 02 Aug 2022 17:41:23: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:41:23: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:41:23: #1 total tags in treatment: 5195863 INFO @ Tue, 02 Aug 2022 17:41:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:41:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:41:23: #1 tags after filtering in treatment: 4051448 INFO @ Tue, 02 Aug 2022 17:41:23: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:41:23: #1 finished! INFO @ Tue, 02 Aug 2022 17:41:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:41:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:41:24: #2 number of paired peaks: 3795 INFO @ Tue, 02 Aug 2022 17:41:24: start model_add_line... INFO @ Tue, 02 Aug 2022 17:41:24: start X-correlation... INFO @ Tue, 02 Aug 2022 17:41:24: end of X-cor INFO @ Tue, 02 Aug 2022 17:41:24: #2 finished! INFO @ Tue, 02 Aug 2022 17:41:24: #2 predicted fragment length is 238 bps INFO @ Tue, 02 Aug 2022 17:41:24: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 02 Aug 2022 17:41:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.05_model.r WARNING @ Tue, 02 Aug 2022 17:41:24: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:41:24: #2 You may need to consider one of the other alternative d(s): 238 WARNING @ Tue, 02 Aug 2022 17:41:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:41:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:41:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:41:27: 13000000 INFO @ Tue, 02 Aug 2022 17:41:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:41:38: 13000000 INFO @ Tue, 02 Aug 2022 17:41:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.05_summits.bed INFO @ Tue, 02 Aug 2022 17:41:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7150 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:41:44: 14000000 INFO @ Tue, 02 Aug 2022 17:41:54: 14000000 INFO @ Tue, 02 Aug 2022 17:41:57: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:41:57: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:41:57: #1 total tags in treatment: 5195863 INFO @ Tue, 02 Aug 2022 17:41:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:41:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:41:57: #1 tags after filtering in treatment: 4051448 INFO @ Tue, 02 Aug 2022 17:41:57: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:41:57: #1 finished! INFO @ Tue, 02 Aug 2022 17:41:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:41:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:41:58: #2 number of paired peaks: 3795 INFO @ Tue, 02 Aug 2022 17:41:58: start model_add_line... INFO @ Tue, 02 Aug 2022 17:41:58: start X-correlation... INFO @ Tue, 02 Aug 2022 17:41:58: end of X-cor INFO @ Tue, 02 Aug 2022 17:41:58: #2 finished! INFO @ Tue, 02 Aug 2022 17:41:58: #2 predicted fragment length is 238 bps INFO @ Tue, 02 Aug 2022 17:41:58: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 02 Aug 2022 17:41:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.10_model.r WARNING @ Tue, 02 Aug 2022 17:41:58: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:41:58: #2 You may need to consider one of the other alternative d(s): 238 WARNING @ Tue, 02 Aug 2022 17:41:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:41:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:41:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:42:06: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 17:42:06: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 17:42:06: #1 total tags in treatment: 5195863 INFO @ Tue, 02 Aug 2022 17:42:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:42:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 17:42:06: #1 tags after filtering in treatment: 4051448 INFO @ Tue, 02 Aug 2022 17:42:06: #1 Redundant rate of treatment: 0.22 INFO @ Tue, 02 Aug 2022 17:42:06: #1 finished! INFO @ Tue, 02 Aug 2022 17:42:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:42:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:42:06: #2 number of paired peaks: 3795 INFO @ Tue, 02 Aug 2022 17:42:06: start model_add_line... INFO @ Tue, 02 Aug 2022 17:42:06: start X-correlation... INFO @ Tue, 02 Aug 2022 17:42:06: end of X-cor INFO @ Tue, 02 Aug 2022 17:42:06: #2 finished! INFO @ Tue, 02 Aug 2022 17:42:06: #2 predicted fragment length is 238 bps INFO @ Tue, 02 Aug 2022 17:42:06: #2 alternative fragment length(s) may be 238 bps INFO @ Tue, 02 Aug 2022 17:42:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.20_model.r WARNING @ Tue, 02 Aug 2022 17:42:06: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:42:06: #2 You may need to consider one of the other alternative d(s): 238 WARNING @ Tue, 02 Aug 2022 17:42:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:42:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:42:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:42:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:42:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.10_summits.bed INFO @ Tue, 02 Aug 2022 17:42:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4300 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:42:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12175827/SRX12175827.20_summits.bed INFO @ Tue, 02 Aug 2022 17:42:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1961 records, 4 fields): 21 millis CompletedMACS2peakCalling