Job ID = 14171368 SRX = SRX9304587 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 49591860 spots for SRR12837084/SRR12837084.sra Written 49591860 spots for SRR12837084/SRR12837084.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172099 ("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: 00:57:36 49591860 reads; of these: 49591860 (100.00%) were paired; of these: 11131274 (22.45%) aligned concordantly 0 times 32663358 (65.86%) aligned concordantly exactly 1 time 5797228 (11.69%) aligned concordantly >1 times ---- 11131274 pairs aligned concordantly 0 times; of these: 410410 (3.69%) aligned discordantly 1 time ---- 10720864 pairs aligned 0 times concordantly or discordantly; of these: 21441728 mates make up the pairs; of these: 20355976 (94.94%) aligned 0 times 797761 (3.72%) aligned exactly 1 time 287991 (1.34%) aligned >1 times 79.48% overall alignment rate Time searching: 00:57:36 Overall time: 00:57:36 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 36 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] 20876095 / 26397453 = 0.7908 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 12:44:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.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 12:44:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:44:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:44:54: 1000000 INFO @ Sat, 11 Dec 2021 12:44:59: 2000000 INFO @ Sat, 11 Dec 2021 12:45:04: 3000000 INFO @ Sat, 11 Dec 2021 12:45:09: 4000000 INFO @ Sat, 11 Dec 2021 12:45:14: 5000000 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 12:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.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 12:45:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:45:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:45:19: 6000000 INFO @ Sat, 11 Dec 2021 12:45:24: 7000000 INFO @ Sat, 11 Dec 2021 12:45:24: 1000000 INFO @ Sat, 11 Dec 2021 12:45:30: 8000000 INFO @ Sat, 11 Dec 2021 12:45:30: 2000000 INFO @ Sat, 11 Dec 2021 12:45:36: 9000000 INFO @ Sat, 11 Dec 2021 12:45:36: 3000000 INFO @ Sat, 11 Dec 2021 12:45:42: 10000000 INFO @ Sat, 11 Dec 2021 12:45:42: 4000000 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 12:45:47: 5000000 INFO @ Sat, 11 Dec 2021 12:45:47: 11000000 INFO @ Sat, 11 Dec 2021 12:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.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 12:45:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:45:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:45:53: 12000000 INFO @ Sat, 11 Dec 2021 12:45:53: 6000000 INFO @ Sat, 11 Dec 2021 12:45:55: 1000000 INFO @ Sat, 11 Dec 2021 12:45:59: 13000000 INFO @ Sat, 11 Dec 2021 12:45:59: 7000000 INFO @ Sat, 11 Dec 2021 12:46:00: 2000000 INFO @ Sat, 11 Dec 2021 12:46:05: 14000000 INFO @ Sat, 11 Dec 2021 12:46:05: 8000000 INFO @ Sat, 11 Dec 2021 12:46:06: 3000000 INFO @ Sat, 11 Dec 2021 12:46:11: 9000000 INFO @ Sat, 11 Dec 2021 12:46:11: 15000000 INFO @ Sat, 11 Dec 2021 12:46:12: 4000000 INFO @ Sat, 11 Dec 2021 12:46:17: 16000000 INFO @ Sat, 11 Dec 2021 12:46:17: 10000000 INFO @ Sat, 11 Dec 2021 12:46:18: 5000000 INFO @ Sat, 11 Dec 2021 12:46:23: 17000000 INFO @ Sat, 11 Dec 2021 12:46:23: 11000000 INFO @ Sat, 11 Dec 2021 12:46:24: 6000000 INFO @ Sat, 11 Dec 2021 12:46:29: 18000000 INFO @ Sat, 11 Dec 2021 12:46:29: 12000000 INFO @ Sat, 11 Dec 2021 12:46:29: 7000000 INFO @ Sat, 11 Dec 2021 12:46:35: 19000000 INFO @ Sat, 11 Dec 2021 12:46:35: 13000000 INFO @ Sat, 11 Dec 2021 12:46:35: 8000000 INFO @ Sat, 11 Dec 2021 12:46:40: 20000000 INFO @ Sat, 11 Dec 2021 12:46:41: 14000000 INFO @ Sat, 11 Dec 2021 12:46:41: 9000000 INFO @ Sat, 11 Dec 2021 12:46:46: 21000000 INFO @ Sat, 11 Dec 2021 12:46:47: 15000000 INFO @ Sat, 11 Dec 2021 12:46:47: 10000000 INFO @ Sat, 11 Dec 2021 12:46:52: 22000000 INFO @ Sat, 11 Dec 2021 12:46:52: 16000000 INFO @ Sat, 11 Dec 2021 12:46:53: 11000000 INFO @ Sat, 11 Dec 2021 12:46:58: 23000000 INFO @ Sat, 11 Dec 2021 12:46:58: 17000000 INFO @ Sat, 11 Dec 2021 12:46:58: 12000000 INFO @ Sat, 11 Dec 2021 12:47:04: 24000000 INFO @ Sat, 11 Dec 2021 12:47:04: 13000000 INFO @ Sat, 11 Dec 2021 12:47:04: 18000000 INFO @ Sat, 11 Dec 2021 12:47:10: 14000000 INFO @ Sat, 11 Dec 2021 12:47:10: 25000000 INFO @ Sat, 11 Dec 2021 12:47:10: 19000000 INFO @ Sat, 11 Dec 2021 12:47:16: 15000000 INFO @ Sat, 11 Dec 2021 12:47:16: 20000000 INFO @ Sat, 11 Dec 2021 12:47:16: 26000000 INFO @ Sat, 11 Dec 2021 12:47:22: 16000000 INFO @ Sat, 11 Dec 2021 12:47:22: 21000000 INFO @ Sat, 11 Dec 2021 12:47:22: 27000000 INFO @ Sat, 11 Dec 2021 12:47:27: 17000000 INFO @ Sat, 11 Dec 2021 12:47:28: 22000000 INFO @ Sat, 11 Dec 2021 12:47:28: 28000000 INFO @ Sat, 11 Dec 2021 12:47:33: 18000000 INFO @ Sat, 11 Dec 2021 12:47:33: 23000000 INFO @ Sat, 11 Dec 2021 12:47:35: 29000000 INFO @ Sat, 11 Dec 2021 12:47:39: 19000000 INFO @ Sat, 11 Dec 2021 12:47:39: 24000000 INFO @ Sat, 11 Dec 2021 12:47:41: 30000000 INFO @ Sat, 11 Dec 2021 12:47:45: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:47:45: 25000000 INFO @ Sat, 11 Dec 2021 12:47:47: 31000000 INFO @ Sat, 11 Dec 2021 12:47:50: 21000000 INFO @ Sat, 11 Dec 2021 12:47:51: 26000000 INFO @ Sat, 11 Dec 2021 12:47:53: 32000000 INFO @ Sat, 11 Dec 2021 12:47:56: 22000000 INFO @ Sat, 11 Dec 2021 12:47:57: 27000000 INFO @ Sat, 11 Dec 2021 12:47:59: 33000000 INFO @ Sat, 11 Dec 2021 12:48:02: 23000000 INFO @ Sat, 11 Dec 2021 12:48:03: 28000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:48:05: 34000000 INFO @ Sat, 11 Dec 2021 12:48:08: 24000000 INFO @ Sat, 11 Dec 2021 12:48:10: 29000000 INFO @ Sat, 11 Dec 2021 12:48:11: 35000000 INFO @ Sat, 11 Dec 2021 12:48:14: 25000000 INFO @ Sat, 11 Dec 2021 12:48:16: 30000000 INFO @ Sat, 11 Dec 2021 12:48:17: 36000000 INFO @ Sat, 11 Dec 2021 12:48:20: 26000000 INFO @ Sat, 11 Dec 2021 12:48:22: 31000000 INFO @ Sat, 11 Dec 2021 12:48:22: 37000000 INFO @ Sat, 11 Dec 2021 12:48:23: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:48:23: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:48:23: #1 total tags in treatment: 17678384 INFO @ Sat, 11 Dec 2021 12:48:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:48:23: #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 12:48:23: #1 tags after filtering in treatment: 5441119 INFO @ Sat, 11 Dec 2021 12:48:23: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 11 Dec 2021 12:48:23: #1 finished! INFO @ Sat, 11 Dec 2021 12:48:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:48:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:48:24: #2 number of paired peaks: 6059 INFO @ Sat, 11 Dec 2021 12:48:24: start model_add_line... INFO @ Sat, 11 Dec 2021 12:48:24: start X-correlation... INFO @ Sat, 11 Dec 2021 12:48:24: end of X-cor INFO @ Sat, 11 Dec 2021 12:48:24: #2 finished! INFO @ Sat, 11 Dec 2021 12:48:24: #2 predicted fragment length is 89 bps INFO @ Sat, 11 Dec 2021 12:48:24: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 11 Dec 2021 12:48:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.05_model.r WARNING @ Sat, 11 Dec 2021 12:48:24: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:48:24: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 11 Dec 2021 12:48:24: #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 12:48:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:48:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:48:26: 27000000 INFO @ Sat, 11 Dec 2021 12:48:28: 32000000 INFO @ Sat, 11 Dec 2021 12:48:32: 28000000 INFO @ Sat, 11 Dec 2021 12:48:34: 33000000 INFO @ Sat, 11 Dec 2021 12:48:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:48:38: 29000000 INFO @ Sat, 11 Dec 2021 12:48:40: 34000000 INFO @ Sat, 11 Dec 2021 12:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.05_summits.bed INFO @ Sat, 11 Dec 2021 12:48:42: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15250 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:48:44: 30000000 INFO @ Sat, 11 Dec 2021 12:48:46: 35000000 INFO @ Sat, 11 Dec 2021 12:48:51: 31000000 INFO @ Sat, 11 Dec 2021 12:48:51: 36000000 INFO @ Sat, 11 Dec 2021 12:48:56: 32000000 INFO @ Sat, 11 Dec 2021 12:48:57: 37000000 INFO @ Sat, 11 Dec 2021 12:48:58: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:48:58: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:48:58: #1 total tags in treatment: 17678384 INFO @ Sat, 11 Dec 2021 12:48:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:48:58: #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 12:48:58: #1 tags after filtering in treatment: 5441119 INFO @ Sat, 11 Dec 2021 12:48:58: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 11 Dec 2021 12:48:58: #1 finished! INFO @ Sat, 11 Dec 2021 12:48:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:48:59: #2 number of paired peaks: 6059 INFO @ Sat, 11 Dec 2021 12:48:59: start model_add_line... INFO @ Sat, 11 Dec 2021 12:48:59: start X-correlation... INFO @ Sat, 11 Dec 2021 12:48:59: end of X-cor INFO @ Sat, 11 Dec 2021 12:48:59: #2 finished! INFO @ Sat, 11 Dec 2021 12:48:59: #2 predicted fragment length is 89 bps INFO @ Sat, 11 Dec 2021 12:48:59: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 11 Dec 2021 12:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.10_model.r WARNING @ Sat, 11 Dec 2021 12:48:59: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:48:59: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 11 Dec 2021 12:48:59: #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 12:48:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:49:02: 33000000 INFO @ Sat, 11 Dec 2021 12:49:07: 34000000 INFO @ Sat, 11 Dec 2021 12:49:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:49:12: 35000000 INFO @ Sat, 11 Dec 2021 12:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.10_summits.bed INFO @ Sat, 11 Dec 2021 12:49:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9898 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:49:17: 36000000 INFO @ Sat, 11 Dec 2021 12:49:22: 37000000 INFO @ Sat, 11 Dec 2021 12:49:23: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:49:23: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:49:23: #1 total tags in treatment: 17678384 INFO @ Sat, 11 Dec 2021 12:49:23: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:49:23: #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 12:49:23: #1 tags after filtering in treatment: 5441119 INFO @ Sat, 11 Dec 2021 12:49:23: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 11 Dec 2021 12:49:23: #1 finished! INFO @ Sat, 11 Dec 2021 12:49:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:49:24: #2 number of paired peaks: 6059 INFO @ Sat, 11 Dec 2021 12:49:24: start model_add_line... INFO @ Sat, 11 Dec 2021 12:49:24: start X-correlation... INFO @ Sat, 11 Dec 2021 12:49:24: end of X-cor INFO @ Sat, 11 Dec 2021 12:49:24: #2 finished! INFO @ Sat, 11 Dec 2021 12:49:24: #2 predicted fragment length is 89 bps INFO @ Sat, 11 Dec 2021 12:49:24: #2 alternative fragment length(s) may be 89 bps INFO @ Sat, 11 Dec 2021 12:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.20_model.r WARNING @ Sat, 11 Dec 2021 12:49:24: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:49:24: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Sat, 11 Dec 2021 12:49:24: #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 12:49:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:49:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:49:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:49:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:49:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:49:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304587/SRX9304587.20_summits.bed INFO @ Sat, 11 Dec 2021 12:49:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4246 records, 4 fields): 5 millis CompletedMACS2peakCalling