Job ID = 14167059 SRX = SRX10412048 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31050056 spots for SRR14035710/SRR14035710.sra Written 31050056 spots for SRR14035710/SRR14035710.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167632 ("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: 01:05:21 31050056 reads; of these: 31050056 (100.00%) were paired; of these: 15292043 (49.25%) aligned concordantly 0 times 13823116 (44.52%) aligned concordantly exactly 1 time 1934897 (6.23%) aligned concordantly >1 times ---- 15292043 pairs aligned concordantly 0 times; of these: 4598917 (30.07%) aligned discordantly 1 time ---- 10693126 pairs aligned 0 times concordantly or discordantly; of these: 21386252 mates make up the pairs; of these: 19097235 (89.30%) aligned 0 times 1117981 (5.23%) aligned exactly 1 time 1171036 (5.48%) aligned >1 times 69.25% overall alignment rate Time searching: 01:05:21 Overall time: 01:05:21 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] 4158664 / 20273590 = 0.2051 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 10:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.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 10:56:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:56:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:56:57: 1000000 INFO @ Fri, 10 Dec 2021 10:57:06: 2000000 INFO @ Fri, 10 Dec 2021 10:57:15: 3000000 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 10:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.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 10:57:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:57:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:57:24: 4000000 INFO @ Fri, 10 Dec 2021 10:57:29: 1000000 INFO @ Fri, 10 Dec 2021 10:57:35: 5000000 INFO @ Fri, 10 Dec 2021 10:57:40: 2000000 INFO @ Fri, 10 Dec 2021 10:57:45: 6000000 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 @ Fri, 10 Dec 2021 10:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.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 10:57:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:57:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:57:51: 3000000 INFO @ Fri, 10 Dec 2021 10:57:56: 7000000 INFO @ Fri, 10 Dec 2021 10:57:59: 1000000 INFO @ Fri, 10 Dec 2021 10:58:01: 4000000 INFO @ Fri, 10 Dec 2021 10:58:07: 8000000 INFO @ Fri, 10 Dec 2021 10:58:10: 2000000 INFO @ Fri, 10 Dec 2021 10:58:12: 5000000 INFO @ Fri, 10 Dec 2021 10:58:18: 9000000 INFO @ Fri, 10 Dec 2021 10:58:20: 3000000 INFO @ Fri, 10 Dec 2021 10:58:23: 6000000 INFO @ Fri, 10 Dec 2021 10:58:29: 10000000 INFO @ Fri, 10 Dec 2021 10:58:31: 4000000 INFO @ Fri, 10 Dec 2021 10:58:33: 7000000 INFO @ Fri, 10 Dec 2021 10:58:40: 11000000 INFO @ Fri, 10 Dec 2021 10:58:41: 5000000 INFO @ Fri, 10 Dec 2021 10:58:44: 8000000 INFO @ Fri, 10 Dec 2021 10:58:50: 12000000 INFO @ Fri, 10 Dec 2021 10:58:52: 6000000 INFO @ Fri, 10 Dec 2021 10:58:54: 9000000 INFO @ Fri, 10 Dec 2021 10:59:01: 13000000 INFO @ Fri, 10 Dec 2021 10:59:02: 7000000 INFO @ Fri, 10 Dec 2021 10:59:05: 10000000 INFO @ Fri, 10 Dec 2021 10:59:11: 14000000 INFO @ Fri, 10 Dec 2021 10:59:13: 8000000 INFO @ Fri, 10 Dec 2021 10:59:16: 11000000 INFO @ Fri, 10 Dec 2021 10:59:22: 15000000 INFO @ Fri, 10 Dec 2021 10:59:23: 9000000 INFO @ Fri, 10 Dec 2021 10:59:26: 12000000 INFO @ Fri, 10 Dec 2021 10:59:33: 16000000 INFO @ Fri, 10 Dec 2021 10:59:34: 10000000 INFO @ Fri, 10 Dec 2021 10:59:37: 13000000 INFO @ Fri, 10 Dec 2021 10:59:43: 17000000 INFO @ Fri, 10 Dec 2021 10:59:44: 11000000 INFO @ Fri, 10 Dec 2021 10:59:47: 14000000 INFO @ Fri, 10 Dec 2021 10:59:54: 18000000 INFO @ Fri, 10 Dec 2021 10:59:55: 12000000 INFO @ Fri, 10 Dec 2021 10:59:58: 15000000 INFO @ Fri, 10 Dec 2021 11:00:04: 19000000 INFO @ Fri, 10 Dec 2021 11:00:06: 13000000 INFO @ Fri, 10 Dec 2021 11:00:09: 16000000 INFO @ Fri, 10 Dec 2021 11:00:15: 20000000 INFO @ Fri, 10 Dec 2021 11:00:16: 14000000 INFO @ Fri, 10 Dec 2021 11:00:20: 17000000 INFO @ Fri, 10 Dec 2021 11:00:25: 21000000 INFO @ Fri, 10 Dec 2021 11:00:27: 15000000 INFO @ Fri, 10 Dec 2021 11:00:31: 18000000 INFO @ Fri, 10 Dec 2021 11:00:36: 22000000 INFO @ Fri, 10 Dec 2021 11:00:38: 16000000 INFO @ Fri, 10 Dec 2021 11:00:42: 19000000 INFO @ Fri, 10 Dec 2021 11:00:46: 23000000 INFO @ Fri, 10 Dec 2021 11:00:49: 17000000 INFO @ Fri, 10 Dec 2021 11:00:52: 20000000 INFO @ Fri, 10 Dec 2021 11:00:57: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:01:00: 18000000 INFO @ Fri, 10 Dec 2021 11:01:03: 21000000 INFO @ Fri, 10 Dec 2021 11:01:08: 25000000 INFO @ Fri, 10 Dec 2021 11:01:10: 19000000 INFO @ Fri, 10 Dec 2021 11:01:14: 22000000 INFO @ Fri, 10 Dec 2021 11:01:19: 26000000 INFO @ Fri, 10 Dec 2021 11:01:21: 20000000 INFO @ Fri, 10 Dec 2021 11:01:25: 23000000 INFO @ Fri, 10 Dec 2021 11:01:30: 27000000 INFO @ Fri, 10 Dec 2021 11:01:31: 21000000 INFO @ Fri, 10 Dec 2021 11:01:35: 24000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:01:40: 28000000 INFO @ Fri, 10 Dec 2021 11:01:42: 22000000 INFO @ Fri, 10 Dec 2021 11:01:46: 25000000 INFO @ Fri, 10 Dec 2021 11:01:51: 29000000 INFO @ Fri, 10 Dec 2021 11:01:52: 23000000 INFO @ Fri, 10 Dec 2021 11:01:57: 26000000 INFO @ Fri, 10 Dec 2021 11:02:02: 30000000 INFO @ Fri, 10 Dec 2021 11:02:03: 24000000 INFO @ Fri, 10 Dec 2021 11:02:08: 27000000 INFO @ Fri, 10 Dec 2021 11:02:13: 31000000 INFO @ Fri, 10 Dec 2021 11:02:14: 25000000 INFO @ Fri, 10 Dec 2021 11:02:19: 28000000 INFO @ Fri, 10 Dec 2021 11:02:24: 32000000 INFO @ Fri, 10 Dec 2021 11:02:25: 26000000 INFO @ Fri, 10 Dec 2021 11:02:30: 29000000 INFO @ Fri, 10 Dec 2021 11:02:35: 33000000 INFO @ Fri, 10 Dec 2021 11:02:35: 27000000 INFO @ Fri, 10 Dec 2021 11:02:41: 30000000 INFO @ Fri, 10 Dec 2021 11:02:45: 34000000 INFO @ Fri, 10 Dec 2021 11:02:46: 28000000 INFO @ Fri, 10 Dec 2021 11:02:52: 31000000 INFO @ Fri, 10 Dec 2021 11:02:53: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:02:53: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:02:53: #1 total tags in treatment: 12367877 INFO @ Fri, 10 Dec 2021 11:02:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:02:53: #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 11:02:53: #1 tags after filtering in treatment: 7605741 INFO @ Fri, 10 Dec 2021 11:02:53: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 10 Dec 2021 11:02:53: #1 finished! INFO @ Fri, 10 Dec 2021 11:02:53: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:02:54: #2 number of paired peaks: 5209 INFO @ Fri, 10 Dec 2021 11:02:54: start model_add_line... INFO @ Fri, 10 Dec 2021 11:02:54: start X-correlation... INFO @ Fri, 10 Dec 2021 11:02:54: end of X-cor INFO @ Fri, 10 Dec 2021 11:02:54: #2 finished! INFO @ Fri, 10 Dec 2021 11:02:54: #2 predicted fragment length is 254 bps INFO @ Fri, 10 Dec 2021 11:02:54: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 10 Dec 2021 11:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.05_model.r WARNING @ Fri, 10 Dec 2021 11:02:54: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:02:54: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Fri, 10 Dec 2021 11:02:54: #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 11:02:54: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:02:57: 29000000 INFO @ Fri, 10 Dec 2021 11:03:03: 32000000 INFO @ Fri, 10 Dec 2021 11:03:08: 30000000 INFO @ Fri, 10 Dec 2021 11:03:14: 33000000 INFO @ Fri, 10 Dec 2021 11:03:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:03:19: 31000000 INFO @ Fri, 10 Dec 2021 11:03:25: 34000000 INFO @ Fri, 10 Dec 2021 11:03:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:03:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:03:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.05_summits.bed INFO @ Fri, 10 Dec 2021 11:03:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9782 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:03:29: 32000000 INFO @ Fri, 10 Dec 2021 11:03:32: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:03:32: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:03:32: #1 total tags in treatment: 12367877 INFO @ Fri, 10 Dec 2021 11:03:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:03:32: #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 11:03:32: #1 tags after filtering in treatment: 7605741 INFO @ Fri, 10 Dec 2021 11:03:32: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 10 Dec 2021 11:03:32: #1 finished! INFO @ Fri, 10 Dec 2021 11:03:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:03:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:03:33: #2 number of paired peaks: 5209 INFO @ Fri, 10 Dec 2021 11:03:33: start model_add_line... INFO @ Fri, 10 Dec 2021 11:03:33: start X-correlation... INFO @ Fri, 10 Dec 2021 11:03:33: end of X-cor INFO @ Fri, 10 Dec 2021 11:03:33: #2 finished! INFO @ Fri, 10 Dec 2021 11:03:33: #2 predicted fragment length is 254 bps INFO @ Fri, 10 Dec 2021 11:03:33: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 10 Dec 2021 11:03:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.10_model.r WARNING @ Fri, 10 Dec 2021 11:03:33: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:03:33: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Fri, 10 Dec 2021 11:03:33: #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 11:03:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:03:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:03:40: 33000000 INFO @ Fri, 10 Dec 2021 11:03:49: 34000000 INFO @ Fri, 10 Dec 2021 11:03:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:03:56: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:03:56: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:03:56: #1 total tags in treatment: 12367877 INFO @ Fri, 10 Dec 2021 11:03:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:03:56: #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 11:03:56: #1 tags after filtering in treatment: 7605741 INFO @ Fri, 10 Dec 2021 11:03:56: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 10 Dec 2021 11:03:56: #1 finished! INFO @ Fri, 10 Dec 2021 11:03:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:03:57: #2 number of paired peaks: 5209 INFO @ Fri, 10 Dec 2021 11:03:57: start model_add_line... INFO @ Fri, 10 Dec 2021 11:03:57: start X-correlation... INFO @ Fri, 10 Dec 2021 11:03:57: end of X-cor INFO @ Fri, 10 Dec 2021 11:03:57: #2 finished! INFO @ Fri, 10 Dec 2021 11:03:57: #2 predicted fragment length is 254 bps INFO @ Fri, 10 Dec 2021 11:03:57: #2 alternative fragment length(s) may be 254 bps INFO @ Fri, 10 Dec 2021 11:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.20_model.r WARNING @ Fri, 10 Dec 2021 11:03:57: #2 Since the d (254) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:03:57: #2 You may need to consider one of the other alternative d(s): 254 WARNING @ Fri, 10 Dec 2021 11:03:57: #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 11:03:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:03:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.10_summits.bed INFO @ Fri, 10 Dec 2021 11:04:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6990 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:04:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:04:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412048/SRX10412048.20_summits.bed INFO @ Fri, 10 Dec 2021 11:04:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4231 records, 4 fields): 6 millis CompletedMACS2peakCalling