Job ID = 6626569 SRX = SRX7224559 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19530336 spots for SRR10541145/SRR10541145.sra Written 19530336 spots for SRR10541145/SRR10541145.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626739 ("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: 00:22:44 19530336 reads; of these: 19530336 (100.00%) were paired; of these: 1001392 (5.13%) aligned concordantly 0 times 17452383 (89.36%) aligned concordantly exactly 1 time 1076561 (5.51%) aligned concordantly >1 times ---- 1001392 pairs aligned concordantly 0 times; of these: 39453 (3.94%) aligned discordantly 1 time ---- 961939 pairs aligned 0 times concordantly or discordantly; of these: 1923878 mates make up the pairs; of these: 1361797 (70.78%) aligned 0 times 446674 (23.22%) aligned exactly 1 time 115407 (6.00%) aligned >1 times 96.51% overall alignment rate Time searching: 00:22:45 Overall time: 00:22:45 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 16 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] 1007581 / 18530201 = 0.0544 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.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, 14 Jul 2020 08:10:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:10:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:11:05: 1000000 INFO @ Tue, 14 Jul 2020 08:11:12: 2000000 INFO @ Tue, 14 Jul 2020 08:11:19: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:11:26: 4000000 INFO @ Tue, 14 Jul 2020 08:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.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, 14 Jul 2020 08:11:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:11:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:11:31: 5000000 INFO @ Tue, 14 Jul 2020 08:11:32: 1000000 INFO @ Tue, 14 Jul 2020 08:11:36: 6000000 INFO @ Tue, 14 Jul 2020 08:11:37: 2000000 INFO @ Tue, 14 Jul 2020 08:11:41: 7000000 INFO @ Tue, 14 Jul 2020 08:11:42: 3000000 INFO @ Tue, 14 Jul 2020 08:11:46: 8000000 INFO @ Tue, 14 Jul 2020 08:11:47: 4000000 INFO @ Tue, 14 Jul 2020 08:11:51: 9000000 INFO @ Tue, 14 Jul 2020 08:11:52: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:11:56: 10000000 INFO @ Tue, 14 Jul 2020 08:11:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.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, 14 Jul 2020 08:11:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:11:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:11:58: 6000000 INFO @ Tue, 14 Jul 2020 08:12:02: 11000000 INFO @ Tue, 14 Jul 2020 08:12:03: 1000000 INFO @ Tue, 14 Jul 2020 08:12:03: 7000000 INFO @ Tue, 14 Jul 2020 08:12:07: 12000000 INFO @ Tue, 14 Jul 2020 08:12:08: 8000000 INFO @ Tue, 14 Jul 2020 08:12:08: 2000000 INFO @ Tue, 14 Jul 2020 08:12:13: 9000000 INFO @ Tue, 14 Jul 2020 08:12:16: 13000000 INFO @ Tue, 14 Jul 2020 08:12:17: 3000000 INFO @ Tue, 14 Jul 2020 08:12:18: 10000000 INFO @ Tue, 14 Jul 2020 08:12:23: 11000000 INFO @ Tue, 14 Jul 2020 08:12:24: 14000000 INFO @ Tue, 14 Jul 2020 08:12:26: 4000000 INFO @ Tue, 14 Jul 2020 08:12:29: 12000000 INFO @ Tue, 14 Jul 2020 08:12:33: 15000000 INFO @ Tue, 14 Jul 2020 08:12:34: 13000000 INFO @ Tue, 14 Jul 2020 08:12:34: 5000000 INFO @ Tue, 14 Jul 2020 08:12:39: 14000000 INFO @ Tue, 14 Jul 2020 08:12:42: 16000000 INFO @ Tue, 14 Jul 2020 08:12:43: 6000000 INFO @ Tue, 14 Jul 2020 08:12:44: 15000000 INFO @ Tue, 14 Jul 2020 08:12:49: 16000000 INFO @ Tue, 14 Jul 2020 08:12:50: 17000000 INFO @ Tue, 14 Jul 2020 08:12:52: 7000000 INFO @ Tue, 14 Jul 2020 08:12:54: 17000000 INFO @ Tue, 14 Jul 2020 08:12:59: 18000000 INFO @ Tue, 14 Jul 2020 08:13:00: 18000000 INFO @ Tue, 14 Jul 2020 08:13:00: 8000000 INFO @ Tue, 14 Jul 2020 08:13:05: 19000000 INFO @ Tue, 14 Jul 2020 08:13:08: 19000000 INFO @ Tue, 14 Jul 2020 08:13:09: 9000000 INFO @ Tue, 14 Jul 2020 08:13:11: 20000000 INFO @ Tue, 14 Jul 2020 08:13:16: 20000000 INFO @ Tue, 14 Jul 2020 08:13:16: 21000000 INFO @ Tue, 14 Jul 2020 08:13:17: 10000000 INFO @ Tue, 14 Jul 2020 08:13:21: 21000000 INFO @ Tue, 14 Jul 2020 08:13:21: 22000000 INFO @ Tue, 14 Jul 2020 08:13:22: 11000000 INFO @ Tue, 14 Jul 2020 08:13:27: 23000000 INFO @ Tue, 14 Jul 2020 08:13:27: 22000000 INFO @ Tue, 14 Jul 2020 08:13:28: 12000000 INFO @ Tue, 14 Jul 2020 08:13:32: 24000000 INFO @ Tue, 14 Jul 2020 08:13:32: 23000000 INFO @ Tue, 14 Jul 2020 08:13:33: 13000000 INFO @ Tue, 14 Jul 2020 08:13:37: 25000000 INFO @ Tue, 14 Jul 2020 08:13:37: 24000000 INFO @ Tue, 14 Jul 2020 08:13:39: 14000000 INFO @ Tue, 14 Jul 2020 08:13:42: 26000000 INFO @ Tue, 14 Jul 2020 08:13:45: 25000000 INFO @ Tue, 14 Jul 2020 08:13:47: 15000000 INFO @ Tue, 14 Jul 2020 08:13:47: 27000000 INFO @ Tue, 14 Jul 2020 08:13:52: 28000000 INFO @ Tue, 14 Jul 2020 08:13:54: 26000000 INFO @ Tue, 14 Jul 2020 08:13:55: 16000000 INFO @ Tue, 14 Jul 2020 08:13:58: 29000000 INFO @ Tue, 14 Jul 2020 08:14:02: 27000000 INFO @ Tue, 14 Jul 2020 08:14:03: 30000000 INFO @ Tue, 14 Jul 2020 08:14:04: 17000000 INFO @ Tue, 14 Jul 2020 08:14:08: 31000000 INFO @ Tue, 14 Jul 2020 08:14:10: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:14:12: 18000000 INFO @ Tue, 14 Jul 2020 08:14:13: 32000000 INFO @ Tue, 14 Jul 2020 08:14:16: 29000000 INFO @ Tue, 14 Jul 2020 08:14:17: 19000000 INFO @ Tue, 14 Jul 2020 08:14:18: 33000000 INFO @ Tue, 14 Jul 2020 08:14:22: 30000000 INFO @ Tue, 14 Jul 2020 08:14:23: 20000000 INFO @ Tue, 14 Jul 2020 08:14:24: 34000000 INFO @ Tue, 14 Jul 2020 08:14:27: 31000000 INFO @ Tue, 14 Jul 2020 08:14:28: 21000000 INFO @ Tue, 14 Jul 2020 08:14:29: 35000000 INFO @ Tue, 14 Jul 2020 08:14:33: 32000000 INFO @ Tue, 14 Jul 2020 08:14:33: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:14:33: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:14:33: #1 total tags in treatment: 17521966 INFO @ Tue, 14 Jul 2020 08:14:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:14:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:14:33: #1 tags after filtering in treatment: 13043795 INFO @ Tue, 14 Jul 2020 08:14:33: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 14 Jul 2020 08:14:33: #1 finished! INFO @ Tue, 14 Jul 2020 08:14:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:14:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:14:33: 22000000 INFO @ Tue, 14 Jul 2020 08:14:35: #2 number of paired peaks: 13318 INFO @ Tue, 14 Jul 2020 08:14:35: start model_add_line... INFO @ Tue, 14 Jul 2020 08:14:35: start X-correlation... INFO @ Tue, 14 Jul 2020 08:14:35: end of X-cor INFO @ Tue, 14 Jul 2020 08:14:35: #2 finished! INFO @ Tue, 14 Jul 2020 08:14:35: #2 predicted fragment length is 135 bps INFO @ Tue, 14 Jul 2020 08:14:35: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 14 Jul 2020 08:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.10_model.r WARNING @ Tue, 14 Jul 2020 08:14:35: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:14:35: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Tue, 14 Jul 2020 08:14:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:14:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:14:38: 33000000 INFO @ Tue, 14 Jul 2020 08:14:39: 23000000 INFO @ Tue, 14 Jul 2020 08:14:43: 34000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:14:44: 24000000 INFO @ Tue, 14 Jul 2020 08:14:48: 35000000 INFO @ Tue, 14 Jul 2020 08:14:49: 25000000 INFO @ Tue, 14 Jul 2020 08:14:52: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:14:52: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:14:52: #1 total tags in treatment: 17521966 INFO @ Tue, 14 Jul 2020 08:14:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:14:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:14:52: #1 tags after filtering in treatment: 13043795 INFO @ Tue, 14 Jul 2020 08:14:52: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 14 Jul 2020 08:14:52: #1 finished! INFO @ Tue, 14 Jul 2020 08:14:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:14:54: #2 number of paired peaks: 13318 INFO @ Tue, 14 Jul 2020 08:14:54: start model_add_line... INFO @ Tue, 14 Jul 2020 08:14:54: 26000000 INFO @ Tue, 14 Jul 2020 08:14:54: start X-correlation... INFO @ Tue, 14 Jul 2020 08:14:54: end of X-cor INFO @ Tue, 14 Jul 2020 08:14:54: #2 finished! INFO @ Tue, 14 Jul 2020 08:14:54: #2 predicted fragment length is 135 bps INFO @ Tue, 14 Jul 2020 08:14:54: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 14 Jul 2020 08:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.05_model.r WARNING @ Tue, 14 Jul 2020 08:14:54: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:14:54: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Tue, 14 Jul 2020 08:14:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:14:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:14:59: 27000000 INFO @ Tue, 14 Jul 2020 08:15:04: 28000000 INFO @ Tue, 14 Jul 2020 08:15:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:15:09: 29000000 INFO @ Tue, 14 Jul 2020 08:15:14: 30000000 INFO @ Tue, 14 Jul 2020 08:15:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:15:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:15:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.10_summits.bed INFO @ Tue, 14 Jul 2020 08:15:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8650 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:15:19: 31000000 INFO @ Tue, 14 Jul 2020 08:15:24: 32000000 INFO @ Tue, 14 Jul 2020 08:15:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:15:29: 33000000 INFO @ Tue, 14 Jul 2020 08:15:34: 34000000 INFO @ Tue, 14 Jul 2020 08:15:39: 35000000 INFO @ Tue, 14 Jul 2020 08:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:15:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.05_summits.bed INFO @ Tue, 14 Jul 2020 08:15:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9411 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:15:43: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:15:43: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:15:43: #1 total tags in treatment: 17521966 INFO @ Tue, 14 Jul 2020 08:15:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:15:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:15:43: #1 tags after filtering in treatment: 13043795 INFO @ Tue, 14 Jul 2020 08:15:43: #1 Redundant rate of treatment: 0.26 INFO @ Tue, 14 Jul 2020 08:15:43: #1 finished! INFO @ Tue, 14 Jul 2020 08:15:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:15:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:15:45: #2 number of paired peaks: 13318 INFO @ Tue, 14 Jul 2020 08:15:45: start model_add_line... INFO @ Tue, 14 Jul 2020 08:15:45: start X-correlation... INFO @ Tue, 14 Jul 2020 08:15:45: end of X-cor INFO @ Tue, 14 Jul 2020 08:15:45: #2 finished! INFO @ Tue, 14 Jul 2020 08:15:45: #2 predicted fragment length is 135 bps INFO @ Tue, 14 Jul 2020 08:15:45: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 14 Jul 2020 08:15:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.20_model.r WARNING @ Tue, 14 Jul 2020 08:15:45: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:15:45: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Tue, 14 Jul 2020 08:15:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:15:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:15:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:16:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:16:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:16:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:16:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224559/SRX7224559.20_summits.bed INFO @ Tue, 14 Jul 2020 08:16:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7504 records, 4 fields): 8 millis CompletedMACS2peakCalling