Job ID = 16439411 SRX = SRX11245075 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T06:05:12 prefetch.2.10.7: 1) Downloading 'SRR14932340'... 2022-08-02T06:05:12 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T06:06:17 prefetch.2.10.7: HTTPS download succeed 2022-08-02T06:06:17 prefetch.2.10.7: 1) 'SRR14932340' was downloaded successfully 2022-08-02T06:06:17 prefetch.2.10.7: 'SRR14932340' has 0 unresolved dependencies Read 24849174 spots for SRR14932340/SRR14932340.sra Written 24849174 spots for SRR14932340/SRR14932340.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440256 ("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: 02:20:21 24849174 reads; of these: 24849174 (100.00%) were paired; of these: 8632117 (34.74%) aligned concordantly 0 times 11297054 (45.46%) aligned concordantly exactly 1 time 4920003 (19.80%) aligned concordantly >1 times ---- 8632117 pairs aligned concordantly 0 times; of these: 2290506 (26.53%) aligned discordantly 1 time ---- 6341611 pairs aligned 0 times concordantly or discordantly; of these: 12683222 mates make up the pairs; of these: 10354652 (81.64%) aligned 0 times 589458 (4.65%) aligned exactly 1 time 1739112 (13.71%) aligned >1 times 79.16% overall alignment rate Time searching: 02:20:21 Overall time: 02:20:21 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 32 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] 4829351 / 18377867 = 0.2628 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 17:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.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 17:50:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:50:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:50:59: 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 17:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.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 17:51:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:51:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:51:17: 2000000 INFO @ Tue, 02 Aug 2022 17:51:27: 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 17:51:36: 3000000 INFO @ Tue, 02 Aug 2022 17:51:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.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 17:51:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:51:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:51:46: 2000000 INFO @ Tue, 02 Aug 2022 17:51:55: 4000000 INFO @ Tue, 02 Aug 2022 17:51:56: 1000000 INFO @ Tue, 02 Aug 2022 17:52:04: 3000000 INFO @ Tue, 02 Aug 2022 17:52:14: 2000000 INFO @ Tue, 02 Aug 2022 17:52:16: 5000000 INFO @ Tue, 02 Aug 2022 17:52:23: 4000000 INFO @ Tue, 02 Aug 2022 17:52:31: 3000000 INFO @ Tue, 02 Aug 2022 17:52:40: 6000000 INFO @ Tue, 02 Aug 2022 17:52:46: 5000000 INFO @ Tue, 02 Aug 2022 17:52:54: 4000000 INFO @ Tue, 02 Aug 2022 17:53:01: 7000000 INFO @ Tue, 02 Aug 2022 17:53:04: 6000000 INFO @ Tue, 02 Aug 2022 17:53:14: 5000000 INFO @ Tue, 02 Aug 2022 17:53:21: 8000000 INFO @ Tue, 02 Aug 2022 17:53:22: 7000000 INFO @ Tue, 02 Aug 2022 17:53:34: 6000000 INFO @ Tue, 02 Aug 2022 17:53:42: 9000000 INFO @ Tue, 02 Aug 2022 17:53:43: 8000000 INFO @ Tue, 02 Aug 2022 17:53:53: 7000000 INFO @ Tue, 02 Aug 2022 17:54:04: 10000000 INFO @ Tue, 02 Aug 2022 17:54:04: 9000000 INFO @ Tue, 02 Aug 2022 17:54:13: 8000000 INFO @ Tue, 02 Aug 2022 17:54:24: 11000000 INFO @ Tue, 02 Aug 2022 17:54:25: 10000000 INFO @ Tue, 02 Aug 2022 17:54:33: 9000000 INFO @ Tue, 02 Aug 2022 17:54:45: 11000000 INFO @ Tue, 02 Aug 2022 17:54:45: 12000000 INFO @ Tue, 02 Aug 2022 17:54:53: 10000000 INFO @ Tue, 02 Aug 2022 17:55:05: 12000000 INFO @ Tue, 02 Aug 2022 17:55:06: 13000000 INFO @ Tue, 02 Aug 2022 17:55:13: 11000000 INFO @ Tue, 02 Aug 2022 17:55:25: 14000000 INFO @ Tue, 02 Aug 2022 17:55:26: 13000000 INFO @ Tue, 02 Aug 2022 17:55:33: 12000000 INFO @ Tue, 02 Aug 2022 17:55:44: 15000000 INFO @ Tue, 02 Aug 2022 17:55:47: 14000000 INFO @ Tue, 02 Aug 2022 17:55:52: 13000000 INFO @ Tue, 02 Aug 2022 17:56:03: 16000000 INFO @ Tue, 02 Aug 2022 17:56:06: 15000000 INFO @ Tue, 02 Aug 2022 17:56:12: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:56:21: 17000000 INFO @ Tue, 02 Aug 2022 17:56:24: 16000000 INFO @ Tue, 02 Aug 2022 17:56:32: 15000000 INFO @ Tue, 02 Aug 2022 17:56:39: 18000000 INFO @ Tue, 02 Aug 2022 17:56:43: 17000000 INFO @ Tue, 02 Aug 2022 17:56:51: 16000000 INFO @ Tue, 02 Aug 2022 17:56:56: 19000000 INFO @ Tue, 02 Aug 2022 17:57:00: 18000000 INFO @ Tue, 02 Aug 2022 17:57:09: 17000000 INFO @ Tue, 02 Aug 2022 17:57:15: 20000000 INFO @ Tue, 02 Aug 2022 17:57:17: 19000000 INFO @ Tue, 02 Aug 2022 17:57:27: 18000000 INFO @ Tue, 02 Aug 2022 17:57:34: 21000000 INFO @ Tue, 02 Aug 2022 17:57:36: 20000000 INFO @ Tue, 02 Aug 2022 17:57:44: 19000000 INFO @ Tue, 02 Aug 2022 17:57:52: 22000000 INFO @ Tue, 02 Aug 2022 17:57:53: 21000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:58:02: 20000000 INFO @ Tue, 02 Aug 2022 17:58:12: 23000000 INFO @ Tue, 02 Aug 2022 17:58:12: 22000000 INFO @ Tue, 02 Aug 2022 17:58:20: 21000000 INFO @ Tue, 02 Aug 2022 17:58:31: 23000000 INFO @ Tue, 02 Aug 2022 17:58:31: 24000000 INFO @ Tue, 02 Aug 2022 17:58:39: 22000000 INFO @ Tue, 02 Aug 2022 17:58:49: 24000000 INFO @ Tue, 02 Aug 2022 17:58:50: 25000000 INFO @ Tue, 02 Aug 2022 17:58:58: 23000000 INFO @ Tue, 02 Aug 2022 17:59:08: 25000000 INFO @ Tue, 02 Aug 2022 17:59:09: 26000000 INFO @ Tue, 02 Aug 2022 17:59:17: 24000000 INFO @ Tue, 02 Aug 2022 17:59:26: 26000000 INFO @ Tue, 02 Aug 2022 17:59:28: 27000000 INFO @ Tue, 02 Aug 2022 17:59:35: 25000000 INFO @ Tue, 02 Aug 2022 17:59:45: 27000000 INFO @ Tue, 02 Aug 2022 17:59:47: 28000000 INFO @ Tue, 02 Aug 2022 17:59:54: 26000000 INFO @ Tue, 02 Aug 2022 18:00:02: 28000000 INFO @ Tue, 02 Aug 2022 18:00:05: 29000000 INFO @ Tue, 02 Aug 2022 18:00:13: 27000000 INFO @ Tue, 02 Aug 2022 18:00:18: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:00:18: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:00:18: #1 total tags in treatment: 11961397 INFO @ Tue, 02 Aug 2022 18:00:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:00:18: #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 18:00:18: #1 tags after filtering in treatment: 11276872 INFO @ Tue, 02 Aug 2022 18:00:18: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 18:00:18: #1 finished! INFO @ Tue, 02 Aug 2022 18:00:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:00:19: 29000000 INFO @ Tue, 02 Aug 2022 18:00:19: #2 number of paired peaks: 253 WARNING @ Tue, 02 Aug 2022 18:00:19: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 02 Aug 2022 18:00:19: start model_add_line... INFO @ Tue, 02 Aug 2022 18:00:20: start X-correlation... INFO @ Tue, 02 Aug 2022 18:00:20: end of X-cor INFO @ Tue, 02 Aug 2022 18:00:20: #2 finished! INFO @ Tue, 02 Aug 2022 18:00:20: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 18:00:20: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 18:00:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.05_model.r WARNING @ Tue, 02 Aug 2022 18:00:20: #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 18:00:20: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 18:00:20: #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 18:00:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:00:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:00:30: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:00:30: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:00:30: #1 total tags in treatment: 11961397 INFO @ Tue, 02 Aug 2022 18:00:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:00:30: #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 18:00:31: #1 tags after filtering in treatment: 11276872 INFO @ Tue, 02 Aug 2022 18:00:31: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 18:00:31: #1 finished! INFO @ Tue, 02 Aug 2022 18:00:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:00:31: 28000000 INFO @ Tue, 02 Aug 2022 18:00:32: #2 number of paired peaks: 253 WARNING @ Tue, 02 Aug 2022 18:00:32: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 02 Aug 2022 18:00:32: start model_add_line... INFO @ Tue, 02 Aug 2022 18:00:32: start X-correlation... INFO @ Tue, 02 Aug 2022 18:00:32: end of X-cor INFO @ Tue, 02 Aug 2022 18:00:32: #2 finished! INFO @ Tue, 02 Aug 2022 18:00:32: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 18:00:32: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 18:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.10_model.r WARNING @ Tue, 02 Aug 2022 18:00:32: #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 18:00:32: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 18:00:32: #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 18:00:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:00:49: 29000000 INFO @ Tue, 02 Aug 2022 18:00:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:01:00: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:01:00: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:01:00: #1 total tags in treatment: 11961397 INFO @ Tue, 02 Aug 2022 18:01:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:01:00: #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 18:01:01: #1 tags after filtering in treatment: 11276872 INFO @ Tue, 02 Aug 2022 18:01:01: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 02 Aug 2022 18:01:01: #1 finished! INFO @ Tue, 02 Aug 2022 18:01:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:01:02: #2 number of paired peaks: 253 WARNING @ Tue, 02 Aug 2022 18:01:02: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Tue, 02 Aug 2022 18:01:02: start model_add_line... INFO @ Tue, 02 Aug 2022 18:01:02: start X-correlation... INFO @ Tue, 02 Aug 2022 18:01:02: end of X-cor INFO @ Tue, 02 Aug 2022 18:01:02: #2 finished! INFO @ Tue, 02 Aug 2022 18:01:02: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 18:01:02: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 18:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.20_model.r WARNING @ Tue, 02 Aug 2022 18:01:02: #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 18:01:02: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 18:01:02: #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 18:01:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:01:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.05_summits.bed INFO @ Tue, 02 Aug 2022 18:01:18: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4614 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.10_summits.bed INFO @ Tue, 02 Aug 2022 18:01:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2354 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:01:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11245075/SRX11245075.20_summits.bed INFO @ Tue, 02 Aug 2022 18:01:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1036 records, 4 fields): 70 millis CompletedMACS2peakCalling