Job ID = 14171790 SRX = SRX9008838 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13991415 spots for SRR12518310/SRR12518310.sra Written 13991415 spots for SRR12518310/SRR12518310.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172347 ("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: 00:31:47 13991415 reads; of these: 13991415 (100.00%) were paired; of these: 1499400 (10.72%) aligned concordantly 0 times 9809616 (70.11%) aligned concordantly exactly 1 time 2682399 (19.17%) aligned concordantly >1 times ---- 1499400 pairs aligned concordantly 0 times; of these: 518274 (34.57%) aligned discordantly 1 time ---- 981126 pairs aligned 0 times concordantly or discordantly; of these: 1962252 mates make up the pairs; of these: 1330147 (67.79%) aligned 0 times 332051 (16.92%) aligned exactly 1 time 300054 (15.29%) aligned >1 times 95.25% overall alignment rate Time searching: 00:31:47 Overall time: 00:31:47 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 12 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] 954541 / 12960113 = 0.0737 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.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 @ Sat, 11 Dec 2021 13:32:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:32:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:32:28: 1000000 INFO @ Sat, 11 Dec 2021 13:32:35: 2000000 INFO @ Sat, 11 Dec 2021 13:32:41: 3000000 INFO @ Sat, 11 Dec 2021 13:32:48: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:32:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.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 @ Sat, 11 Dec 2021 13:32:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:32:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:32:55: 5000000 INFO @ Sat, 11 Dec 2021 13:32:59: 1000000 INFO @ Sat, 11 Dec 2021 13:33:02: 6000000 INFO @ Sat, 11 Dec 2021 13:33:07: 2000000 INFO @ Sat, 11 Dec 2021 13:33:10: 7000000 INFO @ Sat, 11 Dec 2021 13:33:15: 3000000 INFO @ Sat, 11 Dec 2021 13:33:18: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:33:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.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 @ Sat, 11 Dec 2021 13:33:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:33:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:33:23: 4000000 INFO @ Sat, 11 Dec 2021 13:33:26: 9000000 INFO @ Sat, 11 Dec 2021 13:33:30: 1000000 INFO @ Sat, 11 Dec 2021 13:33:31: 5000000 INFO @ Sat, 11 Dec 2021 13:33:35: 10000000 INFO @ Sat, 11 Dec 2021 13:33:39: 2000000 INFO @ Sat, 11 Dec 2021 13:33:40: 6000000 INFO @ Sat, 11 Dec 2021 13:33:44: 11000000 INFO @ Sat, 11 Dec 2021 13:33:47: 3000000 INFO @ Sat, 11 Dec 2021 13:33:49: 7000000 INFO @ Sat, 11 Dec 2021 13:33:52: 12000000 INFO @ Sat, 11 Dec 2021 13:33:56: 4000000 INFO @ Sat, 11 Dec 2021 13:33:57: 8000000 INFO @ Sat, 11 Dec 2021 13:34:00: 13000000 INFO @ Sat, 11 Dec 2021 13:34:04: 5000000 INFO @ Sat, 11 Dec 2021 13:34:06: 9000000 INFO @ Sat, 11 Dec 2021 13:34:09: 14000000 INFO @ Sat, 11 Dec 2021 13:34:12: 6000000 INFO @ Sat, 11 Dec 2021 13:34:14: 10000000 INFO @ Sat, 11 Dec 2021 13:34:17: 15000000 INFO @ Sat, 11 Dec 2021 13:34:20: 7000000 INFO @ Sat, 11 Dec 2021 13:34:22: 11000000 INFO @ Sat, 11 Dec 2021 13:34:25: 16000000 INFO @ Sat, 11 Dec 2021 13:34:28: 8000000 INFO @ Sat, 11 Dec 2021 13:34:30: 12000000 INFO @ Sat, 11 Dec 2021 13:34:33: 17000000 INFO @ Sat, 11 Dec 2021 13:34:37: 9000000 INFO @ Sat, 11 Dec 2021 13:34:39: 13000000 INFO @ Sat, 11 Dec 2021 13:34:41: 18000000 INFO @ Sat, 11 Dec 2021 13:34:45: 10000000 INFO @ Sat, 11 Dec 2021 13:34:47: 14000000 INFO @ Sat, 11 Dec 2021 13:34:49: 19000000 INFO @ Sat, 11 Dec 2021 13:34:53: 11000000 INFO @ Sat, 11 Dec 2021 13:34:55: 15000000 INFO @ Sat, 11 Dec 2021 13:34:57: 20000000 INFO @ Sat, 11 Dec 2021 13:35:01: 12000000 INFO @ Sat, 11 Dec 2021 13:35:02: 16000000 INFO @ Sat, 11 Dec 2021 13:35:05: 21000000 INFO @ Sat, 11 Dec 2021 13:35:09: 13000000 INFO @ Sat, 11 Dec 2021 13:35:10: 17000000 INFO @ Sat, 11 Dec 2021 13:35:13: 22000000 INFO @ Sat, 11 Dec 2021 13:35:17: 14000000 INFO @ Sat, 11 Dec 2021 13:35:19: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:35:22: 23000000 INFO @ Sat, 11 Dec 2021 13:35:25: 15000000 INFO @ Sat, 11 Dec 2021 13:35:27: 19000000 INFO @ Sat, 11 Dec 2021 13:35:30: 24000000 INFO @ Sat, 11 Dec 2021 13:35:33: 16000000 INFO @ Sat, 11 Dec 2021 13:35:36: 20000000 INFO @ Sat, 11 Dec 2021 13:35:36: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:35:36: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:35:36: #1 total tags in treatment: 11572906 INFO @ Sat, 11 Dec 2021 13:35:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:35:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:35:37: #1 tags after filtering in treatment: 11003815 INFO @ Sat, 11 Dec 2021 13:35:37: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:35:37: #1 finished! INFO @ Sat, 11 Dec 2021 13:35:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:35:37: #2 number of paired peaks: 227 WARNING @ Sat, 11 Dec 2021 13:35:37: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 11 Dec 2021 13:35:37: start model_add_line... INFO @ Sat, 11 Dec 2021 13:35:37: start X-correlation... INFO @ Sat, 11 Dec 2021 13:35:37: end of X-cor INFO @ Sat, 11 Dec 2021 13:35:37: #2 finished! INFO @ Sat, 11 Dec 2021 13:35:37: #2 predicted fragment length is 198 bps INFO @ Sat, 11 Dec 2021 13:35:37: #2 alternative fragment length(s) may be 3,179,198 bps INFO @ Sat, 11 Dec 2021 13:35:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.05_model.r WARNING @ Sat, 11 Dec 2021 13:35:37: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:35:37: #2 You may need to consider one of the other alternative d(s): 3,179,198 WARNING @ Sat, 11 Dec 2021 13:35:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:35:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:35:42: 17000000 INFO @ Sat, 11 Dec 2021 13:35:44: 21000000 INFO @ Sat, 11 Dec 2021 13:35:50: 18000000 INFO @ Sat, 11 Dec 2021 13:35:52: 22000000 INFO @ Sat, 11 Dec 2021 13:35:58: 19000000 INFO @ Sat, 11 Dec 2021 13:35:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:36:00: 23000000 INFO @ Sat, 11 Dec 2021 13:36:06: 20000000 INFO @ Sat, 11 Dec 2021 13:36:08: 24000000 INFO @ Sat, 11 Dec 2021 13:36:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:36:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.05_summits.bed INFO @ Sat, 11 Dec 2021 13:36:09: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1723 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:36:14: 21000000 INFO @ Sat, 11 Dec 2021 13:36:14: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:36:14: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:36:14: #1 total tags in treatment: 11572906 INFO @ Sat, 11 Dec 2021 13:36:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:36:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:36:14: #1 tags after filtering in treatment: 11003815 INFO @ Sat, 11 Dec 2021 13:36:14: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:36:14: #1 finished! INFO @ Sat, 11 Dec 2021 13:36:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:36:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:36:15: #2 number of paired peaks: 227 WARNING @ Sat, 11 Dec 2021 13:36:15: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 11 Dec 2021 13:36:15: start model_add_line... INFO @ Sat, 11 Dec 2021 13:36:15: start X-correlation... INFO @ Sat, 11 Dec 2021 13:36:15: end of X-cor INFO @ Sat, 11 Dec 2021 13:36:15: #2 finished! INFO @ Sat, 11 Dec 2021 13:36:15: #2 predicted fragment length is 198 bps INFO @ Sat, 11 Dec 2021 13:36:15: #2 alternative fragment length(s) may be 3,179,198 bps INFO @ Sat, 11 Dec 2021 13:36:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.10_model.r WARNING @ Sat, 11 Dec 2021 13:36:15: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:36:15: #2 You may need to consider one of the other alternative d(s): 3,179,198 WARNING @ Sat, 11 Dec 2021 13:36:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:36:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:36:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:36:21: 22000000 INFO @ Sat, 11 Dec 2021 13:36:29: 23000000 INFO @ Sat, 11 Dec 2021 13:36:36: 24000000 INFO @ Sat, 11 Dec 2021 13:36:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:36:41: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:36:41: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:36:41: #1 total tags in treatment: 11572906 INFO @ Sat, 11 Dec 2021 13:36:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:36:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:36:41: #1 tags after filtering in treatment: 11003815 INFO @ Sat, 11 Dec 2021 13:36:41: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:36:41: #1 finished! INFO @ Sat, 11 Dec 2021 13:36:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:36:42: #2 number of paired peaks: 227 WARNING @ Sat, 11 Dec 2021 13:36:42: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sat, 11 Dec 2021 13:36:42: start model_add_line... INFO @ Sat, 11 Dec 2021 13:36:42: start X-correlation... INFO @ Sat, 11 Dec 2021 13:36:42: end of X-cor INFO @ Sat, 11 Dec 2021 13:36:42: #2 finished! INFO @ Sat, 11 Dec 2021 13:36:42: #2 predicted fragment length is 198 bps INFO @ Sat, 11 Dec 2021 13:36:42: #2 alternative fragment length(s) may be 3,179,198 bps INFO @ Sat, 11 Dec 2021 13:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.20_model.r WARNING @ Sat, 11 Dec 2021 13:36:42: #2 Since the d (198) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:36:42: #2 You may need to consider one of the other alternative d(s): 3,179,198 WARNING @ Sat, 11 Dec 2021 13:36:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:36:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:36:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:36:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:36:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.10_summits.bed INFO @ Sat, 11 Dec 2021 13:36:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (814 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:37:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:37:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:37:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:37:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008838/SRX9008838.20_summits.bed INFO @ Sat, 11 Dec 2021 13:37:14: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (299 records, 4 fields): 2 millis CompletedMACS2peakCalling