Job ID = 16436262 SRX = SRX12178892 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T02:15:44 prefetch.2.10.7: 1) Downloading 'SRR15888022'... 2022-08-02T02:15:44 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:17:37 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:17:37 prefetch.2.10.7: 1) 'SRR15888022' was downloaded successfully 2022-08-02T02:17:37 prefetch.2.10.7: 'SRR15888022' has 0 unresolved dependencies Read 36909536 spots for SRR15888022/SRR15888022.sra Written 36909536 spots for SRR15888022/SRR15888022.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436984 ("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: 00:45:03 36909536 reads; of these: 36909536 (100.00%) were paired; of these: 13087731 (35.46%) aligned concordantly 0 times 20301877 (55.00%) aligned concordantly exactly 1 time 3519928 (9.54%) aligned concordantly >1 times ---- 13087731 pairs aligned concordantly 0 times; of these: 3619118 (27.65%) aligned discordantly 1 time ---- 9468613 pairs aligned 0 times concordantly or discordantly; of these: 18937226 mates make up the pairs; of these: 15046133 (79.45%) aligned 0 times 2753402 (14.54%) aligned exactly 1 time 1137691 (6.01%) aligned >1 times 79.62% overall alignment rate Time searching: 00:45:04 Overall time: 00:45:04 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 24 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] 11158217 / 27306081 = 0.4086 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 12:23:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.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 12:23:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:23:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:24:08: 1000000 INFO @ Tue, 02 Aug 2022 12:24:18: 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 12:24:27: 3000000 INFO @ Tue, 02 Aug 2022 12:24:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.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 12:24:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:24:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:24:37: 4000000 INFO @ Tue, 02 Aug 2022 12:24:38: 1000000 INFO @ Tue, 02 Aug 2022 12:24:46: 5000000 INFO @ Tue, 02 Aug 2022 12:24:47: 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 12:24:55: 6000000 INFO @ Tue, 02 Aug 2022 12:24:57: 3000000 INFO @ Tue, 02 Aug 2022 12:24:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.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 12:24:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:24:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:25:05: 7000000 INFO @ Tue, 02 Aug 2022 12:25:06: 1000000 INFO @ Tue, 02 Aug 2022 12:25:06: 4000000 INFO @ Tue, 02 Aug 2022 12:25:14: 8000000 INFO @ Tue, 02 Aug 2022 12:25:16: 2000000 INFO @ Tue, 02 Aug 2022 12:25:16: 5000000 INFO @ Tue, 02 Aug 2022 12:25:24: 9000000 INFO @ Tue, 02 Aug 2022 12:25:25: 3000000 INFO @ Tue, 02 Aug 2022 12:25:26: 6000000 INFO @ Tue, 02 Aug 2022 12:25:34: 10000000 INFO @ Tue, 02 Aug 2022 12:25:35: 4000000 INFO @ Tue, 02 Aug 2022 12:25:35: 7000000 INFO @ Tue, 02 Aug 2022 12:25:44: 11000000 INFO @ Tue, 02 Aug 2022 12:25:45: 5000000 INFO @ Tue, 02 Aug 2022 12:25:45: 8000000 INFO @ Tue, 02 Aug 2022 12:25:53: 12000000 INFO @ Tue, 02 Aug 2022 12:25:55: 6000000 INFO @ Tue, 02 Aug 2022 12:25:55: 9000000 INFO @ Tue, 02 Aug 2022 12:26:02: 13000000 INFO @ Tue, 02 Aug 2022 12:26:04: 7000000 INFO @ Tue, 02 Aug 2022 12:26:05: 10000000 INFO @ Tue, 02 Aug 2022 12:26:12: 14000000 INFO @ Tue, 02 Aug 2022 12:26:13: 8000000 INFO @ Tue, 02 Aug 2022 12:26:15: 11000000 INFO @ Tue, 02 Aug 2022 12:26:22: 15000000 INFO @ Tue, 02 Aug 2022 12:26:23: 9000000 INFO @ Tue, 02 Aug 2022 12:26:24: 12000000 INFO @ Tue, 02 Aug 2022 12:26:31: 16000000 INFO @ Tue, 02 Aug 2022 12:26:32: 10000000 INFO @ Tue, 02 Aug 2022 12:26:34: 13000000 INFO @ Tue, 02 Aug 2022 12:26:41: 17000000 INFO @ Tue, 02 Aug 2022 12:26:42: 11000000 INFO @ Tue, 02 Aug 2022 12:26:44: 14000000 INFO @ Tue, 02 Aug 2022 12:26:51: 12000000 INFO @ Tue, 02 Aug 2022 12:26:52: 18000000 INFO @ Tue, 02 Aug 2022 12:26:53: 15000000 INFO @ Tue, 02 Aug 2022 12:27:01: 13000000 INFO @ Tue, 02 Aug 2022 12:27:02: 19000000 INFO @ Tue, 02 Aug 2022 12:27:03: 16000000 INFO @ Tue, 02 Aug 2022 12:27:10: 14000000 INFO @ Tue, 02 Aug 2022 12:27:12: 20000000 INFO @ Tue, 02 Aug 2022 12:27:12: 17000000 INFO @ Tue, 02 Aug 2022 12:27:19: 15000000 INFO @ Tue, 02 Aug 2022 12:27:22: 18000000 INFO @ Tue, 02 Aug 2022 12:27:22: 21000000 INFO @ Tue, 02 Aug 2022 12:27:29: 16000000 INFO @ Tue, 02 Aug 2022 12:27:31: 19000000 INFO @ Tue, 02 Aug 2022 12:27:32: 22000000 INFO @ Tue, 02 Aug 2022 12:27:38: 17000000 INFO @ Tue, 02 Aug 2022 12:27:41: 20000000 INFO @ Tue, 02 Aug 2022 12:27:41: 23000000 INFO @ Tue, 02 Aug 2022 12:27:47: 18000000 INFO @ Tue, 02 Aug 2022 12:27:50: 21000000 INFO @ Tue, 02 Aug 2022 12:27:51: 24000000 INFO @ Tue, 02 Aug 2022 12:27:56: 19000000 INFO @ Tue, 02 Aug 2022 12:27:59: 22000000 INFO @ Tue, 02 Aug 2022 12:28:00: 25000000 INFO @ Tue, 02 Aug 2022 12:28:05: 20000000 INFO @ Tue, 02 Aug 2022 12:28:10: 23000000 INFO @ Tue, 02 Aug 2022 12:28:10: 26000000 INFO @ Tue, 02 Aug 2022 12:28:15: 21000000 INFO @ Tue, 02 Aug 2022 12:28:19: 24000000 INFO @ Tue, 02 Aug 2022 12:28:19: 27000000 INFO @ Tue, 02 Aug 2022 12:28:24: 22000000 INFO @ Tue, 02 Aug 2022 12:28:28: 25000000 INFO @ Tue, 02 Aug 2022 12:28:29: 28000000 INFO @ Tue, 02 Aug 2022 12:28:33: 23000000 INFO @ Tue, 02 Aug 2022 12:28:37: 26000000 INFO @ Tue, 02 Aug 2022 12:28:39: 29000000 INFO @ Tue, 02 Aug 2022 12:28:42: 24000000 INFO @ Tue, 02 Aug 2022 12:28:47: 27000000 INFO @ Tue, 02 Aug 2022 12:28:48: 30000000 INFO @ Tue, 02 Aug 2022 12:28:50: 25000000 INFO @ Tue, 02 Aug 2022 12:28:56: 28000000 INFO @ Tue, 02 Aug 2022 12:28:58: 31000000 INFO @ Tue, 02 Aug 2022 12:28:59: 26000000 INFO @ Tue, 02 Aug 2022 12:29:05: 29000000 INFO @ Tue, 02 Aug 2022 12:29:07: 32000000 INFO @ Tue, 02 Aug 2022 12:29:08: 27000000 INFO @ Tue, 02 Aug 2022 12:29:14: 30000000 INFO @ Tue, 02 Aug 2022 12:29:17: 28000000 INFO @ Tue, 02 Aug 2022 12:29:17: 33000000 INFO @ Tue, 02 Aug 2022 12:29:23: 31000000 INFO @ Tue, 02 Aug 2022 12:29:26: 29000000 INFO @ Tue, 02 Aug 2022 12:29:27: 34000000 INFO @ Tue, 02 Aug 2022 12:29:33: 32000000 INFO @ Tue, 02 Aug 2022 12:29:36: 30000000 INFO @ Tue, 02 Aug 2022 12:29:36: 35000000 INFO @ Tue, 02 Aug 2022 12:29:42: 33000000 INFO @ Tue, 02 Aug 2022 12:29:45: 31000000 INFO @ Tue, 02 Aug 2022 12:29:46: 36000000 INFO @ Tue, 02 Aug 2022 12:29:50: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:29:50: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:29:50: #1 total tags in treatment: 13878827 INFO @ Tue, 02 Aug 2022 12:29:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:29:50: #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 12:29:50: #1 tags after filtering in treatment: 10618832 INFO @ Tue, 02 Aug 2022 12:29:50: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 12:29:50: #1 finished! INFO @ Tue, 02 Aug 2022 12:29:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:29:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:29:51: #2 number of paired peaks: 1028 INFO @ Tue, 02 Aug 2022 12:29:51: start model_add_line... INFO @ Tue, 02 Aug 2022 12:29:51: start X-correlation... INFO @ Tue, 02 Aug 2022 12:29:52: end of X-cor INFO @ Tue, 02 Aug 2022 12:29:52: #2 finished! INFO @ Tue, 02 Aug 2022 12:29:52: #2 predicted fragment length is 36 bps INFO @ Tue, 02 Aug 2022 12:29:52: #2 alternative fragment length(s) may be 4,17,36,43 bps INFO @ Tue, 02 Aug 2022 12:29:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.05_model.r WARNING @ Tue, 02 Aug 2022 12:29:52: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:29:52: #2 You may need to consider one of the other alternative d(s): 4,17,36,43 WARNING @ Tue, 02 Aug 2022 12:29:52: #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 12:29:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:29:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:29:52: 34000000 INFO @ Tue, 02 Aug 2022 12:29:55: 32000000 INFO @ Tue, 02 Aug 2022 12:30:01: 35000000 INFO @ Tue, 02 Aug 2022 12:30:04: 33000000 INFO @ Tue, 02 Aug 2022 12:30:11: 36000000 INFO @ Tue, 02 Aug 2022 12:30:13: 34000000 INFO @ Tue, 02 Aug 2022 12:30:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:30:15: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:30:15: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:30:15: #1 total tags in treatment: 13878827 INFO @ Tue, 02 Aug 2022 12:30:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:30:15: #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 12:30:15: #1 tags after filtering in treatment: 10618832 INFO @ Tue, 02 Aug 2022 12:30:15: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 12:30:15: #1 finished! INFO @ Tue, 02 Aug 2022 12:30:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:30:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:30:16: #2 number of paired peaks: 1028 INFO @ Tue, 02 Aug 2022 12:30:16: start model_add_line... INFO @ Tue, 02 Aug 2022 12:30:16: start X-correlation... INFO @ Tue, 02 Aug 2022 12:30:16: end of X-cor INFO @ Tue, 02 Aug 2022 12:30:16: #2 finished! INFO @ Tue, 02 Aug 2022 12:30:16: #2 predicted fragment length is 36 bps INFO @ Tue, 02 Aug 2022 12:30:16: #2 alternative fragment length(s) may be 4,17,36,43 bps INFO @ Tue, 02 Aug 2022 12:30:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.10_model.r WARNING @ Tue, 02 Aug 2022 12:30:16: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:30:16: #2 You may need to consider one of the other alternative d(s): 4,17,36,43 WARNING @ Tue, 02 Aug 2022 12:30:16: #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 12:30:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:30:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:30:22: 35000000 INFO @ Tue, 02 Aug 2022 12:30:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:30:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:30:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.05_summits.bed INFO @ Tue, 02 Aug 2022 12:30:26: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13951 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:30:31: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:30:35: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:30:35: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:30:35: #1 total tags in treatment: 13878827 INFO @ Tue, 02 Aug 2022 12:30:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:30:35: #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 12:30:35: #1 tags after filtering in treatment: 10618832 INFO @ Tue, 02 Aug 2022 12:30:35: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 12:30:35: #1 finished! INFO @ Tue, 02 Aug 2022 12:30:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:30:36: #2 number of paired peaks: 1028 INFO @ Tue, 02 Aug 2022 12:30:36: start model_add_line... INFO @ Tue, 02 Aug 2022 12:30:36: start X-correlation... INFO @ Tue, 02 Aug 2022 12:30:36: end of X-cor INFO @ Tue, 02 Aug 2022 12:30:36: #2 finished! INFO @ Tue, 02 Aug 2022 12:30:36: #2 predicted fragment length is 36 bps INFO @ Tue, 02 Aug 2022 12:30:36: #2 alternative fragment length(s) may be 4,17,36,43 bps INFO @ Tue, 02 Aug 2022 12:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.20_model.r WARNING @ Tue, 02 Aug 2022 12:30:36: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:30:36: #2 You may need to consider one of the other alternative d(s): 4,17,36,43 WARNING @ Tue, 02 Aug 2022 12:30:36: #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 12:30:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:30:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:30:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:30:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:30:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.10_summits.bed INFO @ Tue, 02 Aug 2022 12:30:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3893 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 12:30:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12178892/SRX12178892.20_summits.bed INFO @ Tue, 02 Aug 2022 12:31:07: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (57 records, 4 fields): 32 millis CompletedMACS2peakCalling BigWig に変換しました。