Job ID = 16440072 SRX = SRX10855784 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21665393 spots for SRR14509971/SRR14509971.sra Written 21665393 spots for SRR14509971/SRR14509971.sra fastq に変換しました。 bowtie でマッピング中... Your job 16441099 ("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: 01:28:31 21665393 reads; of these: 21665393 (100.00%) were paired; of these: 1902854 (8.78%) aligned concordantly 0 times 14468159 (66.78%) aligned concordantly exactly 1 time 5294380 (24.44%) aligned concordantly >1 times ---- 1902854 pairs aligned concordantly 0 times; of these: 444580 (23.36%) aligned discordantly 1 time ---- 1458274 pairs aligned 0 times concordantly or discordantly; of these: 2916548 mates make up the pairs; of these: 1966402 (67.42%) aligned 0 times 571775 (19.60%) aligned exactly 1 time 378371 (12.97%) aligned >1 times 95.46% overall alignment rate Time searching: 01:28:32 Overall time: 01:28:32 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 20 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] 5212534 / 20076378 = 0.2596 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 18:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.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 18:53:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:53:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:54:11: 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 18:54:26: 2000000 INFO @ Tue, 02 Aug 2022 18:54:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.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 18:54:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:54:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:54:41: 3000000 INFO @ Tue, 02 Aug 2022 18:54:42: 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 18:54:57: 2000000 INFO @ Tue, 02 Aug 2022 18:54:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.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 18:54:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:54:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:54:57: 4000000 INFO @ Tue, 02 Aug 2022 18:55:12: 3000000 INFO @ Tue, 02 Aug 2022 18:55:14: 5000000 INFO @ Tue, 02 Aug 2022 18:55:14: 1000000 INFO @ Tue, 02 Aug 2022 18:55:27: 4000000 INFO @ Tue, 02 Aug 2022 18:55:30: 6000000 INFO @ Tue, 02 Aug 2022 18:55:30: 2000000 INFO @ Tue, 02 Aug 2022 18:55:43: 5000000 INFO @ Tue, 02 Aug 2022 18:55:47: 7000000 INFO @ Tue, 02 Aug 2022 18:55:47: 3000000 INFO @ Tue, 02 Aug 2022 18:55:57: 6000000 INFO @ Tue, 02 Aug 2022 18:56:02: 8000000 INFO @ Tue, 02 Aug 2022 18:56:03: 4000000 INFO @ Tue, 02 Aug 2022 18:56:12: 7000000 INFO @ Tue, 02 Aug 2022 18:56:19: 9000000 INFO @ Tue, 02 Aug 2022 18:56:19: 5000000 INFO @ Tue, 02 Aug 2022 18:56:27: 8000000 INFO @ Tue, 02 Aug 2022 18:56:35: 10000000 INFO @ Tue, 02 Aug 2022 18:56:36: 6000000 INFO @ Tue, 02 Aug 2022 18:56:42: 9000000 INFO @ Tue, 02 Aug 2022 18:56:52: 11000000 INFO @ Tue, 02 Aug 2022 18:56:53: 7000000 INFO @ Tue, 02 Aug 2022 18:56:57: 10000000 INFO @ Tue, 02 Aug 2022 18:57:09: 12000000 INFO @ Tue, 02 Aug 2022 18:57:09: 8000000 INFO @ Tue, 02 Aug 2022 18:57:11: 11000000 INFO @ Tue, 02 Aug 2022 18:57:24: 12000000 INFO @ Tue, 02 Aug 2022 18:57:26: 13000000 INFO @ Tue, 02 Aug 2022 18:57:26: 9000000 INFO @ Tue, 02 Aug 2022 18:57:37: 13000000 INFO @ Tue, 02 Aug 2022 18:57:42: 14000000 INFO @ Tue, 02 Aug 2022 18:57:44: 10000000 INFO @ Tue, 02 Aug 2022 18:57:53: 14000000 INFO @ Tue, 02 Aug 2022 18:57:57: 15000000 INFO @ Tue, 02 Aug 2022 18:58:00: 11000000 INFO @ Tue, 02 Aug 2022 18:58:08: 15000000 INFO @ Tue, 02 Aug 2022 18:58:12: 16000000 INFO @ Tue, 02 Aug 2022 18:58:17: 12000000 INFO @ Tue, 02 Aug 2022 18:58:23: 16000000 INFO @ Tue, 02 Aug 2022 18:58:27: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:58:34: 13000000 INFO @ Tue, 02 Aug 2022 18:58:38: 17000000 INFO @ Tue, 02 Aug 2022 18:58:42: 18000000 INFO @ Tue, 02 Aug 2022 18:58:49: 14000000 INFO @ Tue, 02 Aug 2022 18:58:53: 18000000 INFO @ Tue, 02 Aug 2022 18:58:57: 19000000 INFO @ Tue, 02 Aug 2022 18:59:04: 15000000 INFO @ Tue, 02 Aug 2022 18:59:08: 19000000 INFO @ Tue, 02 Aug 2022 18:59:12: 20000000 INFO @ Tue, 02 Aug 2022 18:59:20: 16000000 INFO @ Tue, 02 Aug 2022 18:59:22: 20000000 INFO @ Tue, 02 Aug 2022 18:59:27: 21000000 INFO @ Tue, 02 Aug 2022 18:59:35: 17000000 INFO @ Tue, 02 Aug 2022 18:59:36: 21000000 INFO @ Tue, 02 Aug 2022 18:59:41: 22000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:59:50: 22000000 INFO @ Tue, 02 Aug 2022 18:59:51: 18000000 INFO @ Tue, 02 Aug 2022 18:59:55: 23000000 INFO @ Tue, 02 Aug 2022 19:00:04: 23000000 INFO @ Tue, 02 Aug 2022 19:00:06: 19000000 INFO @ Tue, 02 Aug 2022 19:00:10: 24000000 INFO @ Tue, 02 Aug 2022 19:00:19: 24000000 INFO @ Tue, 02 Aug 2022 19:00:22: 20000000 INFO @ Tue, 02 Aug 2022 19:00:25: 25000000 INFO @ Tue, 02 Aug 2022 19:00:33: 25000000 INFO @ Tue, 02 Aug 2022 19:00:37: 21000000 INFO @ Tue, 02 Aug 2022 19:00:40: 26000000 INFO @ Tue, 02 Aug 2022 19:00:48: 26000000 INFO @ Tue, 02 Aug 2022 19:00:52: 22000000 INFO @ Tue, 02 Aug 2022 19:00:55: 27000000 INFO @ Tue, 02 Aug 2022 19:01:03: 27000000 INFO @ Tue, 02 Aug 2022 19:01:07: 23000000 INFO @ Tue, 02 Aug 2022 19:01:10: 28000000 INFO @ Tue, 02 Aug 2022 19:01:18: 28000000 INFO @ Tue, 02 Aug 2022 19:01:23: 24000000 INFO @ Tue, 02 Aug 2022 19:01:25: 29000000 INFO @ Tue, 02 Aug 2022 19:01:33: 29000000 INFO @ Tue, 02 Aug 2022 19:01:38: 25000000 INFO @ Tue, 02 Aug 2022 19:01:39: 30000000 INFO @ Tue, 02 Aug 2022 19:01:48: 30000000 INFO @ Tue, 02 Aug 2022 19:01:52: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:01:52: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:01:52: #1 total tags in treatment: 14605211 INFO @ Tue, 02 Aug 2022 19:01:52: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:01:52: #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 19:01:53: #1 tags after filtering in treatment: 11096345 INFO @ Tue, 02 Aug 2022 19:01:53: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 19:01:53: #1 finished! INFO @ Tue, 02 Aug 2022 19:01:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:01:54: 26000000 INFO @ Tue, 02 Aug 2022 19:01:54: #2 number of paired peaks: 1698 INFO @ Tue, 02 Aug 2022 19:01:54: start model_add_line... INFO @ Tue, 02 Aug 2022 19:01:54: start X-correlation... INFO @ Tue, 02 Aug 2022 19:01:54: end of X-cor INFO @ Tue, 02 Aug 2022 19:01:54: #2 finished! INFO @ Tue, 02 Aug 2022 19:01:54: #2 predicted fragment length is 167 bps INFO @ Tue, 02 Aug 2022 19:01:54: #2 alternative fragment length(s) may be 1,167 bps INFO @ Tue, 02 Aug 2022 19:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.05_model.r WARNING @ Tue, 02 Aug 2022 19:01:54: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:01:54: #2 You may need to consider one of the other alternative d(s): 1,167 WARNING @ Tue, 02 Aug 2022 19:01:54: #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 19:01:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:02:02: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:02:02: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:02:02: #1 total tags in treatment: 14605211 INFO @ Tue, 02 Aug 2022 19:02:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:02:02: #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 19:02:02: #1 tags after filtering in treatment: 11096345 INFO @ Tue, 02 Aug 2022 19:02:02: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 19:02:02: #1 finished! INFO @ Tue, 02 Aug 2022 19:02:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:02:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:02:03: #2 number of paired peaks: 1698 INFO @ Tue, 02 Aug 2022 19:02:03: start model_add_line... INFO @ Tue, 02 Aug 2022 19:02:03: start X-correlation... INFO @ Tue, 02 Aug 2022 19:02:03: end of X-cor INFO @ Tue, 02 Aug 2022 19:02:03: #2 finished! INFO @ Tue, 02 Aug 2022 19:02:03: #2 predicted fragment length is 167 bps INFO @ Tue, 02 Aug 2022 19:02:03: #2 alternative fragment length(s) may be 1,167 bps INFO @ Tue, 02 Aug 2022 19:02:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.10_model.r WARNING @ Tue, 02 Aug 2022 19:02:03: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:02:03: #2 You may need to consider one of the other alternative d(s): 1,167 WARNING @ Tue, 02 Aug 2022 19:02:03: #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 19:02:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:02:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:02:10: 27000000 INFO @ Tue, 02 Aug 2022 19:02:26: 28000000 INFO @ Tue, 02 Aug 2022 19:02:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:02:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:02:43: 29000000 INFO @ Tue, 02 Aug 2022 19:02:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.05_peaks.xls INFO @ Tue, 02 Aug 2022 19:02:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:02:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.05_summits.bed INFO @ Tue, 02 Aug 2022 19:02:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1753 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:02:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.10_peaks.xls INFO @ Tue, 02 Aug 2022 19:02:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:02:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.10_summits.bed INFO @ Tue, 02 Aug 2022 19:02:56: Done! pass1 - making usageList (12 chroms): 3 millis pass2 - checking and writing primary data (748 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:02:59: 30000000 INFO @ Tue, 02 Aug 2022 19:03:14: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:03:14: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:03:14: #1 total tags in treatment: 14605211 INFO @ Tue, 02 Aug 2022 19:03:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:03:14: #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 19:03:15: #1 tags after filtering in treatment: 11096345 INFO @ Tue, 02 Aug 2022 19:03:15: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 02 Aug 2022 19:03:15: #1 finished! INFO @ Tue, 02 Aug 2022 19:03:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:03:16: #2 number of paired peaks: 1698 INFO @ Tue, 02 Aug 2022 19:03:16: start model_add_line... INFO @ Tue, 02 Aug 2022 19:03:16: start X-correlation... INFO @ Tue, 02 Aug 2022 19:03:16: end of X-cor INFO @ Tue, 02 Aug 2022 19:03:16: #2 finished! INFO @ Tue, 02 Aug 2022 19:03:16: #2 predicted fragment length is 167 bps INFO @ Tue, 02 Aug 2022 19:03:16: #2 alternative fragment length(s) may be 1,167 bps INFO @ Tue, 02 Aug 2022 19:03:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.20_model.r WARNING @ Tue, 02 Aug 2022 19:03:16: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:03:16: #2 You may need to consider one of the other alternative d(s): 1,167 WARNING @ Tue, 02 Aug 2022 19:03:16: #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 19:03:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:03:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:03:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.20_peaks.xls INFO @ Tue, 02 Aug 2022 19:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855784/SRX10855784.20_summits.bed INFO @ Tue, 02 Aug 2022 19:04:09: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 3 millis CompletedMACS2peakCalling