Job ID = 14167036 SRX = SRX8694693 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36270875 spots for SRR12180115/SRR12180115.sra Written 36270875 spots for SRR12180115/SRR12180115.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167921 ("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: 02:34:46 36270875 reads; of these: 36270875 (100.00%) were paired; of these: 15208405 (41.93%) aligned concordantly 0 times 15564036 (42.91%) aligned concordantly exactly 1 time 5498434 (15.16%) aligned concordantly >1 times ---- 15208405 pairs aligned concordantly 0 times; of these: 2767561 (18.20%) aligned discordantly 1 time ---- 12440844 pairs aligned 0 times concordantly or discordantly; of these: 24881688 mates make up the pairs; of these: 20648596 (82.99%) aligned 0 times 1539150 (6.19%) aligned exactly 1 time 2693942 (10.83%) aligned >1 times 71.54% overall alignment rate Time searching: 02:34:47 Overall time: 02:34:47 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 40 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] 5510019 / 23627487 = 0.2332 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 @ Fri, 10 Dec 2021 12:14:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.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 @ Fri, 10 Dec 2021 12:14:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:14:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:14:26: 1000000 INFO @ Fri, 10 Dec 2021 12:14:36: 2000000 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 @ Fri, 10 Dec 2021 12:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.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 @ Fri, 10 Dec 2021 12:14:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:14:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:14:48: 3000000 INFO @ Fri, 10 Dec 2021 12:14:59: 1000000 INFO @ Fri, 10 Dec 2021 12:15:01: 4000000 BedGraph に変換中... INFO @ Fri, 10 Dec 2021 12:15:11: 2000000 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 @ Fri, 10 Dec 2021 12:15:14: 5000000 INFO @ Fri, 10 Dec 2021 12:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.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 @ Fri, 10 Dec 2021 12:15:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:15:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:15:23: 3000000 INFO @ Fri, 10 Dec 2021 12:15:26: 6000000 INFO @ Fri, 10 Dec 2021 12:15:30: 1000000 INFO @ Fri, 10 Dec 2021 12:15:36: 4000000 INFO @ Fri, 10 Dec 2021 12:15:39: 7000000 INFO @ Fri, 10 Dec 2021 12:15:42: 2000000 INFO @ Fri, 10 Dec 2021 12:15:49: 5000000 INFO @ Fri, 10 Dec 2021 12:15:52: 8000000 INFO @ Fri, 10 Dec 2021 12:15:55: 3000000 INFO @ Fri, 10 Dec 2021 12:16:02: 6000000 INFO @ Fri, 10 Dec 2021 12:16:05: 9000000 INFO @ Fri, 10 Dec 2021 12:16:08: 4000000 INFO @ Fri, 10 Dec 2021 12:16:15: 7000000 INFO @ Fri, 10 Dec 2021 12:16:18: 10000000 INFO @ Fri, 10 Dec 2021 12:16:21: 5000000 INFO @ Fri, 10 Dec 2021 12:16:27: 8000000 INFO @ Fri, 10 Dec 2021 12:16:30: 11000000 INFO @ Fri, 10 Dec 2021 12:16:34: 6000000 INFO @ Fri, 10 Dec 2021 12:16:40: 9000000 INFO @ Fri, 10 Dec 2021 12:16:49: 12000000 INFO @ Fri, 10 Dec 2021 12:16:51: 7000000 INFO @ Fri, 10 Dec 2021 12:16:58: 10000000 INFO @ Fri, 10 Dec 2021 12:17:03: 13000000 INFO @ Fri, 10 Dec 2021 12:17:05: 8000000 INFO @ Fri, 10 Dec 2021 12:17:11: 11000000 INFO @ Fri, 10 Dec 2021 12:17:15: 14000000 INFO @ Fri, 10 Dec 2021 12:17:17: 9000000 INFO @ Fri, 10 Dec 2021 12:17:23: 12000000 INFO @ Fri, 10 Dec 2021 12:17:28: 15000000 INFO @ Fri, 10 Dec 2021 12:17:30: 10000000 INFO @ Fri, 10 Dec 2021 12:17:35: 13000000 INFO @ Fri, 10 Dec 2021 12:17:41: 16000000 INFO @ Fri, 10 Dec 2021 12:17:43: 11000000 INFO @ Fri, 10 Dec 2021 12:17:48: 14000000 INFO @ Fri, 10 Dec 2021 12:17:54: 17000000 INFO @ Fri, 10 Dec 2021 12:17:56: 12000000 INFO @ Fri, 10 Dec 2021 12:18:00: 15000000 INFO @ Fri, 10 Dec 2021 12:18:07: 18000000 INFO @ Fri, 10 Dec 2021 12:18:08: 13000000 INFO @ Fri, 10 Dec 2021 12:18:13: 16000000 INFO @ Fri, 10 Dec 2021 12:18:20: 19000000 INFO @ Fri, 10 Dec 2021 12:18:20: 14000000 INFO @ Fri, 10 Dec 2021 12:18:26: 17000000 INFO @ Fri, 10 Dec 2021 12:18:32: 20000000 INFO @ Fri, 10 Dec 2021 12:18:33: 15000000 INFO @ Fri, 10 Dec 2021 12:18:39: 18000000 INFO @ Fri, 10 Dec 2021 12:18:45: 21000000 INFO @ Fri, 10 Dec 2021 12:18:46: 16000000 INFO @ Fri, 10 Dec 2021 12:18:52: 19000000 INFO @ Fri, 10 Dec 2021 12:18:57: 22000000 INFO @ Fri, 10 Dec 2021 12:19:00: 17000000 INFO @ Fri, 10 Dec 2021 12:19:05: 20000000 INFO @ Fri, 10 Dec 2021 12:19:10: 23000000 INFO @ Fri, 10 Dec 2021 12:19:12: 18000000 INFO @ Fri, 10 Dec 2021 12:19:20: 21000000 INFO @ Fri, 10 Dec 2021 12:19:23: 24000000 INFO @ Fri, 10 Dec 2021 12:19:24: 19000000 INFO @ Fri, 10 Dec 2021 12:19:33: 22000000 INFO @ Fri, 10 Dec 2021 12:19:36: 25000000 INFO @ Fri, 10 Dec 2021 12:19:38: 20000000 INFO @ Fri, 10 Dec 2021 12:19:46: 23000000 INFO @ Fri, 10 Dec 2021 12:19:49: 26000000 INFO @ Fri, 10 Dec 2021 12:19:50: 21000000 INFO @ Fri, 10 Dec 2021 12:19:58: 24000000 INFO @ Fri, 10 Dec 2021 12:20:02: 27000000 INFO @ Fri, 10 Dec 2021 12:20:03: 22000000 INFO @ Fri, 10 Dec 2021 12:20:10: 25000000 INFO @ Fri, 10 Dec 2021 12:20:15: 28000000 INFO @ Fri, 10 Dec 2021 12:20:16: 23000000 INFO @ Fri, 10 Dec 2021 12:20:24: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:20:30: 29000000 INFO @ Fri, 10 Dec 2021 12:20:30: 24000000 INFO @ Fri, 10 Dec 2021 12:20:37: 27000000 INFO @ Fri, 10 Dec 2021 12:20:42: 25000000 INFO @ Fri, 10 Dec 2021 12:20:42: 30000000 INFO @ Fri, 10 Dec 2021 12:20:49: 28000000 INFO @ Fri, 10 Dec 2021 12:20:54: 26000000 INFO @ Fri, 10 Dec 2021 12:20:55: 31000000 INFO @ Fri, 10 Dec 2021 12:21:01: 29000000 INFO @ Fri, 10 Dec 2021 12:21:07: 27000000 INFO @ Fri, 10 Dec 2021 12:21:08: 32000000 INFO @ Fri, 10 Dec 2021 12:21:14: 30000000 INFO @ Fri, 10 Dec 2021 12:21:21: 33000000 INFO @ Fri, 10 Dec 2021 12:21:21: 28000000 INFO @ Fri, 10 Dec 2021 12:21:27: 31000000 INFO @ Fri, 10 Dec 2021 12:21:33: 29000000 INFO @ Fri, 10 Dec 2021 12:21:33: 34000000 INFO @ Fri, 10 Dec 2021 12:21:39: 32000000 INFO @ Fri, 10 Dec 2021 12:21:45: 35000000 INFO @ Fri, 10 Dec 2021 12:21:45: 30000000 INFO @ Fri, 10 Dec 2021 12:21:52: 33000000 INFO @ Fri, 10 Dec 2021 12:21:58: 36000000 INFO @ Fri, 10 Dec 2021 12:21:58: 31000000 INFO @ Fri, 10 Dec 2021 12:22:05: 34000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:22:10: 37000000 INFO @ Fri, 10 Dec 2021 12:22:11: 32000000 INFO @ Fri, 10 Dec 2021 12:22:18: 35000000 INFO @ Fri, 10 Dec 2021 12:22:23: 38000000 INFO @ Fri, 10 Dec 2021 12:22:24: 33000000 INFO @ Fri, 10 Dec 2021 12:22:31: 36000000 INFO @ Fri, 10 Dec 2021 12:22:36: 39000000 INFO @ Fri, 10 Dec 2021 12:22:37: 34000000 INFO @ Fri, 10 Dec 2021 12:22:43: 37000000 INFO @ Fri, 10 Dec 2021 12:22:49: 35000000 INFO @ Fri, 10 Dec 2021 12:22:49: 40000000 INFO @ Fri, 10 Dec 2021 12:22:56: 38000000 INFO @ Fri, 10 Dec 2021 12:23:00: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 12:23:00: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 12:23:00: #1 total tags in treatment: 16123726 INFO @ Fri, 10 Dec 2021 12:23:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:23:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:23:00: #1 tags after filtering in treatment: 13856525 INFO @ Fri, 10 Dec 2021 12:23:00: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 12:23:00: #1 finished! INFO @ Fri, 10 Dec 2021 12:23:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:23:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:23:01: 36000000 INFO @ Fri, 10 Dec 2021 12:23:01: #2 number of paired peaks: 1711 INFO @ Fri, 10 Dec 2021 12:23:01: start model_add_line... INFO @ Fri, 10 Dec 2021 12:23:01: start X-correlation... INFO @ Fri, 10 Dec 2021 12:23:02: end of X-cor INFO @ Fri, 10 Dec 2021 12:23:02: #2 finished! INFO @ Fri, 10 Dec 2021 12:23:02: #2 predicted fragment length is 226 bps INFO @ Fri, 10 Dec 2021 12:23:02: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 10 Dec 2021 12:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.05_model.r WARNING @ Fri, 10 Dec 2021 12:23:02: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:23:02: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Fri, 10 Dec 2021 12:23:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:23:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:23:09: 39000000 INFO @ Fri, 10 Dec 2021 12:23:12: 37000000 INFO @ Fri, 10 Dec 2021 12:23:20: 40000000 INFO @ Fri, 10 Dec 2021 12:23:23: 38000000 INFO @ Fri, 10 Dec 2021 12:23:30: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 12:23:30: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 12:23:30: #1 total tags in treatment: 16123726 INFO @ Fri, 10 Dec 2021 12:23:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:23:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:23:31: #1 tags after filtering in treatment: 13856525 INFO @ Fri, 10 Dec 2021 12:23:31: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 12:23:31: #1 finished! INFO @ Fri, 10 Dec 2021 12:23:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:23:32: #2 number of paired peaks: 1711 INFO @ Fri, 10 Dec 2021 12:23:32: start model_add_line... INFO @ Fri, 10 Dec 2021 12:23:32: start X-correlation... INFO @ Fri, 10 Dec 2021 12:23:32: end of X-cor INFO @ Fri, 10 Dec 2021 12:23:32: #2 finished! INFO @ Fri, 10 Dec 2021 12:23:32: #2 predicted fragment length is 226 bps INFO @ Fri, 10 Dec 2021 12:23:32: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 10 Dec 2021 12:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.10_model.r WARNING @ Fri, 10 Dec 2021 12:23:32: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:23:32: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Fri, 10 Dec 2021 12:23:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:23:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:23:34: 39000000 INFO @ Fri, 10 Dec 2021 12:23:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:23:49: 40000000 INFO @ Fri, 10 Dec 2021 12:23:58: #1 tag size is determined as 151 bps INFO @ Fri, 10 Dec 2021 12:23:58: #1 tag size = 151 INFO @ Fri, 10 Dec 2021 12:23:58: #1 total tags in treatment: 16123726 INFO @ Fri, 10 Dec 2021 12:23:58: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:23:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:23:58: #1 tags after filtering in treatment: 13856525 INFO @ Fri, 10 Dec 2021 12:23:58: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 10 Dec 2021 12:23:58: #1 finished! INFO @ Fri, 10 Dec 2021 12:23:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:23:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:23:59: #2 number of paired peaks: 1711 INFO @ Fri, 10 Dec 2021 12:23:59: start model_add_line... INFO @ Fri, 10 Dec 2021 12:24:00: start X-correlation... INFO @ Fri, 10 Dec 2021 12:24:00: end of X-cor INFO @ Fri, 10 Dec 2021 12:24:00: #2 finished! INFO @ Fri, 10 Dec 2021 12:24:00: #2 predicted fragment length is 226 bps INFO @ Fri, 10 Dec 2021 12:24:00: #2 alternative fragment length(s) may be 226 bps INFO @ Fri, 10 Dec 2021 12:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.20_model.r WARNING @ Fri, 10 Dec 2021 12:24:00: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:24:00: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Fri, 10 Dec 2021 12:24:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:24:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:24:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:24:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:24:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:24:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.05_summits.bed INFO @ Fri, 10 Dec 2021 12:24:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5364 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:24:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:24:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:24:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:24:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.10_summits.bed INFO @ Fri, 10 Dec 2021 12:24:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3458 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:24:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:24:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:24:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:24:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8694693/SRX8694693.20_summits.bed INFO @ Fri, 10 Dec 2021 12:24:57: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2058 records, 4 fields): 6 millis CompletedMACS2peakCalling