Job ID = 16439423 SRX = SRX11245080 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:07:48 prefetch.2.10.7: 1) Downloading 'SRR14932345'... 2022-08-02T06:07:48 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:08:43 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:08:43 prefetch.2.10.7: 1) 'SRR14932345' was downloaded successfully 2022-08-02T06:08:43 prefetch.2.10.7: 'SRR14932345' has 0 unresolved dependencies Read 27710830 spots for SRR14932345/SRR14932345.sra Written 27710830 spots for SRR14932345/SRR14932345.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440890 ("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: 02:48:20 27710830 reads; of these: 27710830 (100.00%) were paired; of these: 7450072 (26.89%) aligned concordantly 0 times 14557352 (52.53%) aligned concordantly exactly 1 time 5703406 (20.58%) aligned concordantly >1 times ---- 7450072 pairs aligned concordantly 0 times; of these: 2571901 (34.52%) aligned discordantly 1 time ---- 4878171 pairs aligned 0 times concordantly or discordantly; of these: 9756342 mates make up the pairs; of these: 7000927 (71.76%) aligned 0 times 713533 (7.31%) aligned exactly 1 time 2041882 (20.93%) aligned >1 times 87.37% overall alignment rate Time searching: 02:48:20 Overall time: 02:48:20 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 36 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] 6807987 / 22730123 = 0.2995 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 18:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.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 18:22:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:22:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:22:17: 1000000 INFO @ Tue, 02 Aug 2022 18:22:29: 2000000 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 18:22:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.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 18:22:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:22:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:22:40: 3000000 INFO @ Tue, 02 Aug 2022 18:22:47: 1000000 INFO @ Tue, 02 Aug 2022 18:22:52: 4000000 INFO @ Tue, 02 Aug 2022 18:23:01: 2000000 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 18:23:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.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 18:23:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:23:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:23:05: 5000000 INFO @ Tue, 02 Aug 2022 18:23:15: 1000000 INFO @ Tue, 02 Aug 2022 18:23:15: 3000000 INFO @ Tue, 02 Aug 2022 18:23:18: 6000000 INFO @ Tue, 02 Aug 2022 18:23:24: 2000000 INFO @ Tue, 02 Aug 2022 18:23:29: 4000000 INFO @ Tue, 02 Aug 2022 18:23:30: 7000000 INFO @ Tue, 02 Aug 2022 18:23:33: 3000000 INFO @ Tue, 02 Aug 2022 18:23:43: 8000000 INFO @ Tue, 02 Aug 2022 18:23:43: 4000000 INFO @ Tue, 02 Aug 2022 18:23:43: 5000000 INFO @ Tue, 02 Aug 2022 18:23:52: 5000000 INFO @ Tue, 02 Aug 2022 18:23:56: 9000000 INFO @ Tue, 02 Aug 2022 18:23:57: 6000000 INFO @ Tue, 02 Aug 2022 18:24:02: 6000000 INFO @ Tue, 02 Aug 2022 18:24:08: 10000000 INFO @ Tue, 02 Aug 2022 18:24:10: 7000000 INFO @ Tue, 02 Aug 2022 18:24:12: 7000000 INFO @ Tue, 02 Aug 2022 18:24:21: 11000000 INFO @ Tue, 02 Aug 2022 18:24:22: 8000000 INFO @ Tue, 02 Aug 2022 18:24:23: 8000000 INFO @ Tue, 02 Aug 2022 18:24:31: 9000000 INFO @ Tue, 02 Aug 2022 18:24:33: 12000000 INFO @ Tue, 02 Aug 2022 18:24:36: 9000000 INFO @ Tue, 02 Aug 2022 18:24:41: 10000000 INFO @ Tue, 02 Aug 2022 18:24:46: 13000000 INFO @ Tue, 02 Aug 2022 18:24:50: 10000000 INFO @ Tue, 02 Aug 2022 18:24:51: 11000000 INFO @ Tue, 02 Aug 2022 18:24:58: 14000000 INFO @ Tue, 02 Aug 2022 18:25:00: 12000000 INFO @ Tue, 02 Aug 2022 18:25:03: 11000000 INFO @ Tue, 02 Aug 2022 18:25:10: 13000000 INFO @ Tue, 02 Aug 2022 18:25:10: 15000000 INFO @ Tue, 02 Aug 2022 18:25:16: 12000000 INFO @ Tue, 02 Aug 2022 18:25:19: 14000000 INFO @ Tue, 02 Aug 2022 18:25:23: 16000000 INFO @ Tue, 02 Aug 2022 18:25:29: 15000000 INFO @ Tue, 02 Aug 2022 18:25:29: 13000000 INFO @ Tue, 02 Aug 2022 18:25:35: 17000000 INFO @ Tue, 02 Aug 2022 18:25:38: 16000000 INFO @ Tue, 02 Aug 2022 18:25:42: 14000000 INFO @ Tue, 02 Aug 2022 18:25:47: 18000000 INFO @ Tue, 02 Aug 2022 18:25:48: 17000000 INFO @ Tue, 02 Aug 2022 18:25:56: 15000000 INFO @ Tue, 02 Aug 2022 18:25:57: 18000000 INFO @ Tue, 02 Aug 2022 18:26:00: 19000000 INFO @ Tue, 02 Aug 2022 18:26:07: 19000000 INFO @ Tue, 02 Aug 2022 18:26:09: 16000000 INFO @ Tue, 02 Aug 2022 18:26:12: 20000000 INFO @ Tue, 02 Aug 2022 18:26:16: 20000000 INFO @ Tue, 02 Aug 2022 18:26:23: 17000000 INFO @ Tue, 02 Aug 2022 18:26:25: 21000000 INFO @ Tue, 02 Aug 2022 18:26:25: 21000000 INFO @ Tue, 02 Aug 2022 18:26:35: 22000000 INFO @ Tue, 02 Aug 2022 18:26:36: 18000000 INFO @ Tue, 02 Aug 2022 18:26:37: 22000000 INFO @ Tue, 02 Aug 2022 18:26:44: 23000000 INFO @ Tue, 02 Aug 2022 18:26:49: 23000000 INFO @ Tue, 02 Aug 2022 18:26:50: 19000000 INFO @ Tue, 02 Aug 2022 18:26:54: 24000000 INFO @ Tue, 02 Aug 2022 18:27:01: 24000000 INFO @ Tue, 02 Aug 2022 18:27:03: 25000000 INFO @ Tue, 02 Aug 2022 18:27:03: 20000000 INFO @ Tue, 02 Aug 2022 18:27:13: 26000000 INFO @ Tue, 02 Aug 2022 18:27:14: 25000000 INFO @ Tue, 02 Aug 2022 18:27:17: 21000000 INFO @ Tue, 02 Aug 2022 18:27:22: 27000000 INFO @ Tue, 02 Aug 2022 18:27:27: 26000000 INFO @ Tue, 02 Aug 2022 18:27:30: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:27:32: 28000000 INFO @ Tue, 02 Aug 2022 18:27:39: 27000000 INFO @ Tue, 02 Aug 2022 18:27:42: 29000000 INFO @ Tue, 02 Aug 2022 18:27:43: 23000000 INFO @ Tue, 02 Aug 2022 18:27:52: 30000000 INFO @ Tue, 02 Aug 2022 18:27:52: 28000000 INFO @ Tue, 02 Aug 2022 18:27:57: 24000000 INFO @ Tue, 02 Aug 2022 18:28:02: 31000000 INFO @ Tue, 02 Aug 2022 18:28:05: 29000000 INFO @ Tue, 02 Aug 2022 18:28:11: 25000000 INFO @ Tue, 02 Aug 2022 18:28:12: 32000000 INFO @ Tue, 02 Aug 2022 18:28:18: 30000000 INFO @ Tue, 02 Aug 2022 18:28:22: 33000000 INFO @ Tue, 02 Aug 2022 18:28:24: 26000000 INFO @ Tue, 02 Aug 2022 18:28:31: 34000000 INFO @ Tue, 02 Aug 2022 18:28:32: 31000000 INFO @ Tue, 02 Aug 2022 18:28:38: 27000000 INFO @ Tue, 02 Aug 2022 18:28:39: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:28:39: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:28:39: #1 total tags in treatment: 14212601 INFO @ Tue, 02 Aug 2022 18:28:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:28:39: #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 18:28:39: #1 tags after filtering in treatment: 13162071 INFO @ Tue, 02 Aug 2022 18:28:39: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 02 Aug 2022 18:28:39: #1 finished! INFO @ Tue, 02 Aug 2022 18:28:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:28:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:28:40: #2 number of paired peaks: 201 WARNING @ Tue, 02 Aug 2022 18:28:40: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 02 Aug 2022 18:28:40: start model_add_line... INFO @ Tue, 02 Aug 2022 18:28:40: start X-correlation... INFO @ Tue, 02 Aug 2022 18:28:40: end of X-cor INFO @ Tue, 02 Aug 2022 18:28:40: #2 finished! INFO @ Tue, 02 Aug 2022 18:28:40: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 18:28:40: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 18:28:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.20_model.r WARNING @ Tue, 02 Aug 2022 18:28:40: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:28:40: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 18:28:40: #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 18:28:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:28:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:28:45: 32000000 INFO @ Tue, 02 Aug 2022 18:28:51: 28000000 INFO @ Tue, 02 Aug 2022 18:28:58: 33000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:29:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:29:05: 29000000 INFO @ Tue, 02 Aug 2022 18:29:10: 34000000 INFO @ Tue, 02 Aug 2022 18:29:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:29:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:29:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.20_summits.bed INFO @ Tue, 02 Aug 2022 18:29:18: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1044 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:29:20: 30000000 INFO @ Tue, 02 Aug 2022 18:29:20: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:29:20: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:29:20: #1 total tags in treatment: 14212601 INFO @ Tue, 02 Aug 2022 18:29:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:29:20: #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 18:29:21: #1 tags after filtering in treatment: 13162071 INFO @ Tue, 02 Aug 2022 18:29:21: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 02 Aug 2022 18:29:21: #1 finished! INFO @ Tue, 02 Aug 2022 18:29:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:29:22: #2 number of paired peaks: 201 WARNING @ Tue, 02 Aug 2022 18:29:22: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 02 Aug 2022 18:29:22: start model_add_line... INFO @ Tue, 02 Aug 2022 18:29:22: start X-correlation... INFO @ Tue, 02 Aug 2022 18:29:22: end of X-cor INFO @ Tue, 02 Aug 2022 18:29:22: #2 finished! INFO @ Tue, 02 Aug 2022 18:29:22: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 18:29:22: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 18:29:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.05_model.r WARNING @ Tue, 02 Aug 2022 18:29:22: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:29:22: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 18:29:22: #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 18:29:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:29:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:29:35: 31000000 INFO @ Tue, 02 Aug 2022 18:29:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:29:49: 32000000 INFO @ Tue, 02 Aug 2022 18:30:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:30:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:30:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.05_summits.bed INFO @ Tue, 02 Aug 2022 18:30:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5220 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:30:03: 33000000 INFO @ Tue, 02 Aug 2022 18:30:16: 34000000 INFO @ Tue, 02 Aug 2022 18:30:27: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:30:27: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:30:27: #1 total tags in treatment: 14212601 INFO @ Tue, 02 Aug 2022 18:30:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:30:27: #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 18:30:27: #1 tags after filtering in treatment: 13162071 INFO @ Tue, 02 Aug 2022 18:30:27: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 02 Aug 2022 18:30:27: #1 finished! INFO @ Tue, 02 Aug 2022 18:30:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:30:28: #2 number of paired peaks: 201 WARNING @ Tue, 02 Aug 2022 18:30:28: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 02 Aug 2022 18:30:28: start model_add_line... INFO @ Tue, 02 Aug 2022 18:30:28: start X-correlation... INFO @ Tue, 02 Aug 2022 18:30:28: end of X-cor INFO @ Tue, 02 Aug 2022 18:30:28: #2 finished! INFO @ Tue, 02 Aug 2022 18:30:28: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 18:30:28: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 18:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.10_model.r WARNING @ Tue, 02 Aug 2022 18:30:28: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:30:28: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 18:30:28: #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 18:30:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:30:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:31:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:31:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:31:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245080/SRX11245080.10_summits.bed INFO @ Tue, 02 Aug 2022 18:31:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2692 records, 4 fields): 35 millis CompletedMACS2peakCalling