Job ID = 16440068 SRX = SRX10855781 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21360002 spots for SRR14509968/SRR14509968.sra Written 21360002 spots for SRR14509968/SRR14509968.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440675 ("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: 00:45:17 21360002 reads; of these: 21360002 (100.00%) were paired; of these: 2372933 (11.11%) aligned concordantly 0 times 14404895 (67.44%) aligned concordantly exactly 1 time 4582174 (21.45%) aligned concordantly >1 times ---- 2372933 pairs aligned concordantly 0 times; of these: 613845 (25.87%) aligned discordantly 1 time ---- 1759088 pairs aligned 0 times concordantly or discordantly; of these: 3518176 mates make up the pairs; of these: 2322804 (66.02%) aligned 0 times 780064 (22.17%) aligned exactly 1 time 415308 (11.80%) aligned >1 times 94.56% overall alignment rate Time searching: 00:45:17 Overall time: 00:45:17 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] 1882887 / 19476589 = 0.0967 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 17:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.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 17:52:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:52:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:52:06: 1000000 INFO @ Tue, 02 Aug 2022 17:52:12: 2000000 INFO @ Tue, 02 Aug 2022 17:52:17: 3000000 INFO @ Tue, 02 Aug 2022 17:52:23: 4000000 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 17:52:29: 5000000 INFO @ Tue, 02 Aug 2022 17:52:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.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 17:52:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:52:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:52:35: 6000000 INFO @ Tue, 02 Aug 2022 17:52:37: 1000000 INFO @ Tue, 02 Aug 2022 17:52:41: 7000000 INFO @ Tue, 02 Aug 2022 17:52:43: 2000000 INFO @ Tue, 02 Aug 2022 17:52:47: 8000000 INFO @ Tue, 02 Aug 2022 17:52:49: 3000000 INFO @ Tue, 02 Aug 2022 17:52:53: 9000000 INFO @ Tue, 02 Aug 2022 17:52:55: 4000000 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 17:52:59: 10000000 INFO @ Tue, 02 Aug 2022 17:53:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.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 17:53:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:53:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:53:01: 5000000 INFO @ Tue, 02 Aug 2022 17:53:05: 11000000 INFO @ Tue, 02 Aug 2022 17:53:08: 1000000 INFO @ Tue, 02 Aug 2022 17:53:08: 6000000 INFO @ Tue, 02 Aug 2022 17:53:12: 12000000 INFO @ Tue, 02 Aug 2022 17:53:14: 7000000 INFO @ Tue, 02 Aug 2022 17:53:15: 2000000 INFO @ Tue, 02 Aug 2022 17:53:18: 13000000 INFO @ Tue, 02 Aug 2022 17:53:21: 8000000 INFO @ Tue, 02 Aug 2022 17:53:22: 3000000 INFO @ Tue, 02 Aug 2022 17:53:25: 14000000 INFO @ Tue, 02 Aug 2022 17:53:27: 9000000 INFO @ Tue, 02 Aug 2022 17:53:29: 4000000 INFO @ Tue, 02 Aug 2022 17:53:32: 15000000 INFO @ Tue, 02 Aug 2022 17:53:34: 10000000 INFO @ Tue, 02 Aug 2022 17:53:37: 5000000 INFO @ Tue, 02 Aug 2022 17:53:38: 16000000 INFO @ Tue, 02 Aug 2022 17:53:40: 11000000 INFO @ Tue, 02 Aug 2022 17:53:44: 6000000 INFO @ Tue, 02 Aug 2022 17:53:45: 17000000 INFO @ Tue, 02 Aug 2022 17:53:47: 12000000 INFO @ Tue, 02 Aug 2022 17:53:51: 7000000 INFO @ Tue, 02 Aug 2022 17:53:51: 18000000 INFO @ Tue, 02 Aug 2022 17:53:53: 13000000 INFO @ Tue, 02 Aug 2022 17:53:58: 19000000 INFO @ Tue, 02 Aug 2022 17:53:58: 8000000 INFO @ Tue, 02 Aug 2022 17:54:00: 14000000 INFO @ Tue, 02 Aug 2022 17:54:04: 20000000 INFO @ Tue, 02 Aug 2022 17:54:05: 9000000 INFO @ Tue, 02 Aug 2022 17:54:06: 15000000 INFO @ Tue, 02 Aug 2022 17:54:11: 21000000 INFO @ Tue, 02 Aug 2022 17:54:12: 10000000 INFO @ Tue, 02 Aug 2022 17:54:13: 16000000 INFO @ Tue, 02 Aug 2022 17:54:17: 22000000 INFO @ Tue, 02 Aug 2022 17:54:19: 17000000 INFO @ Tue, 02 Aug 2022 17:54:19: 11000000 INFO @ Tue, 02 Aug 2022 17:54:24: 23000000 INFO @ Tue, 02 Aug 2022 17:54:26: 18000000 INFO @ Tue, 02 Aug 2022 17:54:26: 12000000 INFO @ Tue, 02 Aug 2022 17:54:30: 24000000 INFO @ Tue, 02 Aug 2022 17:54:32: 19000000 INFO @ Tue, 02 Aug 2022 17:54:34: 13000000 INFO @ Tue, 02 Aug 2022 17:54:37: 25000000 INFO @ Tue, 02 Aug 2022 17:54:38: 20000000 INFO @ Tue, 02 Aug 2022 17:54:41: 14000000 INFO @ Tue, 02 Aug 2022 17:54:43: 26000000 INFO @ Tue, 02 Aug 2022 17:54:45: 21000000 INFO @ Tue, 02 Aug 2022 17:54:48: 15000000 INFO @ Tue, 02 Aug 2022 17:54:50: 27000000 INFO @ Tue, 02 Aug 2022 17:54:51: 22000000 INFO @ Tue, 02 Aug 2022 17:54:55: 16000000 INFO @ Tue, 02 Aug 2022 17:54:56: 28000000 INFO @ Tue, 02 Aug 2022 17:54:58: 23000000 INFO @ Tue, 02 Aug 2022 17:55:02: 17000000 INFO @ Tue, 02 Aug 2022 17:55:03: 29000000 INFO @ Tue, 02 Aug 2022 17:55:04: 24000000 INFO @ Tue, 02 Aug 2022 17:55:09: 18000000 INFO @ Tue, 02 Aug 2022 17:55:09: 30000000 INFO @ Tue, 02 Aug 2022 17:55:10: 25000000 INFO @ Tue, 02 Aug 2022 17:55:15: 31000000 INFO @ Tue, 02 Aug 2022 17:55:16: 19000000 INFO @ Tue, 02 Aug 2022 17:55:17: 26000000 INFO @ Tue, 02 Aug 2022 17:55:22: 32000000 INFO @ Tue, 02 Aug 2022 17:55:23: 27000000 INFO @ Tue, 02 Aug 2022 17:55:23: 20000000 INFO @ Tue, 02 Aug 2022 17:55:28: 33000000 INFO @ Tue, 02 Aug 2022 17:55:29: 28000000 INFO @ Tue, 02 Aug 2022 17:55:30: 21000000 INFO @ Tue, 02 Aug 2022 17:55:35: 34000000 INFO @ Tue, 02 Aug 2022 17:55:36: 29000000 INFO @ Tue, 02 Aug 2022 17:55:37: 22000000 INFO @ Tue, 02 Aug 2022 17:55:41: 35000000 INFO @ Tue, 02 Aug 2022 17:55:42: 30000000 INFO @ Tue, 02 Aug 2022 17:55:44: 23000000 INFO @ Tue, 02 Aug 2022 17:55:47: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:55:48: 31000000 INFO @ Tue, 02 Aug 2022 17:55:51: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 17:55:51: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 17:55:51: #1 total tags in treatment: 17127747 INFO @ Tue, 02 Aug 2022 17:55:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:55:51: #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 17:55:52: 24000000 INFO @ Tue, 02 Aug 2022 17:55:52: #1 tags after filtering in treatment: 14000050 INFO @ Tue, 02 Aug 2022 17:55:52: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 02 Aug 2022 17:55:52: #1 finished! INFO @ Tue, 02 Aug 2022 17:55:52: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:55:53: #2 number of paired peaks: 150 WARNING @ Tue, 02 Aug 2022 17:55:53: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Tue, 02 Aug 2022 17:55:53: start model_add_line... INFO @ Tue, 02 Aug 2022 17:55:53: start X-correlation... INFO @ Tue, 02 Aug 2022 17:55:53: end of X-cor INFO @ Tue, 02 Aug 2022 17:55:53: #2 finished! INFO @ Tue, 02 Aug 2022 17:55:53: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 17:55:53: #2 alternative fragment length(s) may be 24,47,67,97,121,139,163,252,527,574,592 bps INFO @ Tue, 02 Aug 2022 17:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.05_model.r WARNING @ Tue, 02 Aug 2022 17:55:53: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:55:53: #2 You may need to consider one of the other alternative d(s): 24,47,67,97,121,139,163,252,527,574,592 WARNING @ Tue, 02 Aug 2022 17:55:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 17:55:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:55:55: 32000000 INFO @ Tue, 02 Aug 2022 17:55:59: 25000000 INFO @ Tue, 02 Aug 2022 17:56:01: 33000000 INFO @ Tue, 02 Aug 2022 17:56:06: 26000000 INFO @ Tue, 02 Aug 2022 17:56:07: 34000000 INFO @ Tue, 02 Aug 2022 17:56:13: 27000000 INFO @ Tue, 02 Aug 2022 17:56:14: 35000000 INFO @ Tue, 02 Aug 2022 17:56:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:56:21: 28000000 INFO @ Tue, 02 Aug 2022 17:56:21: 36000000 INFO @ Tue, 02 Aug 2022 17:56:26: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 17:56:26: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 17:56:26: #1 total tags in treatment: 17127747 INFO @ Tue, 02 Aug 2022 17:56:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:56:26: #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 17:56:26: #1 tags after filtering in treatment: 14000050 INFO @ Tue, 02 Aug 2022 17:56:26: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 02 Aug 2022 17:56:26: #1 finished! INFO @ Tue, 02 Aug 2022 17:56:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:56:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:56:27: #2 number of paired peaks: 150 WARNING @ Tue, 02 Aug 2022 17:56:27: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Tue, 02 Aug 2022 17:56:27: start model_add_line... INFO @ Tue, 02 Aug 2022 17:56:27: start X-correlation... INFO @ Tue, 02 Aug 2022 17:56:27: end of X-cor INFO @ Tue, 02 Aug 2022 17:56:27: #2 finished! INFO @ Tue, 02 Aug 2022 17:56:27: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 17:56:27: #2 alternative fragment length(s) may be 24,47,67,97,121,139,163,252,527,574,592 bps INFO @ Tue, 02 Aug 2022 17:56:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.10_model.r WARNING @ Tue, 02 Aug 2022 17:56:27: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:56:27: #2 You may need to consider one of the other alternative d(s): 24,47,67,97,121,139,163,252,527,574,592 WARNING @ Tue, 02 Aug 2022 17:56:27: #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 17:56:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:56:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:56:28: 29000000 INFO @ Tue, 02 Aug 2022 17:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.05_summits.bed INFO @ Tue, 02 Aug 2022 17:56:33: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1100 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:56:35: 30000000 INFO @ Tue, 02 Aug 2022 17:56:42: 31000000 INFO @ Tue, 02 Aug 2022 17:56:49: 32000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:56:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:56:56: 33000000 INFO @ Tue, 02 Aug 2022 17:57:03: 34000000 INFO @ Tue, 02 Aug 2022 17:57:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.10_peaks.xls INFO @ Tue, 02 Aug 2022 17:57:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:57:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.10_summits.bed INFO @ Tue, 02 Aug 2022 17:57:07: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 17:57:10: 35000000 INFO @ Tue, 02 Aug 2022 17:57:17: 36000000 INFO @ Tue, 02 Aug 2022 17:57:21: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 17:57:21: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 17:57:21: #1 total tags in treatment: 17127747 INFO @ Tue, 02 Aug 2022 17:57:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:57:21: #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 17:57:22: #1 tags after filtering in treatment: 14000050 INFO @ Tue, 02 Aug 2022 17:57:22: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 02 Aug 2022 17:57:22: #1 finished! INFO @ Tue, 02 Aug 2022 17:57:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:57:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:57:22: #2 number of paired peaks: 150 WARNING @ Tue, 02 Aug 2022 17:57:22: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Tue, 02 Aug 2022 17:57:22: start model_add_line... INFO @ Tue, 02 Aug 2022 17:57:23: start X-correlation... INFO @ Tue, 02 Aug 2022 17:57:23: end of X-cor INFO @ Tue, 02 Aug 2022 17:57:23: #2 finished! INFO @ Tue, 02 Aug 2022 17:57:23: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 17:57:23: #2 alternative fragment length(s) may be 24,47,67,97,121,139,163,252,527,574,592 bps INFO @ Tue, 02 Aug 2022 17:57:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.20_model.r WARNING @ Tue, 02 Aug 2022 17:57:23: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:57:23: #2 You may need to consider one of the other alternative d(s): 24,47,67,97,121,139,163,252,527,574,592 WARNING @ Tue, 02 Aug 2022 17:57:23: #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 17:57:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:57:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:57:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:58:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:58:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:58:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855781/SRX10855781.20_summits.bed INFO @ Tue, 02 Aug 2022 17:58:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 23 millis CompletedMACS2peakCalling