Job ID = 6626561 SRX = SRX7224530 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18353633 spots for SRR10541174/SRR10541174.sra Written 18353633 spots for SRR10541174/SRR10541174.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626734 ("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: 00:22:55 18353633 reads; of these: 18353633 (100.00%) were paired; of these: 957038 (5.21%) aligned concordantly 0 times 16425021 (89.49%) aligned concordantly exactly 1 time 971574 (5.29%) aligned concordantly >1 times ---- 957038 pairs aligned concordantly 0 times; of these: 104635 (10.93%) aligned discordantly 1 time ---- 852403 pairs aligned 0 times concordantly or discordantly; of these: 1704806 mates make up the pairs; of these: 1109266 (65.07%) aligned 0 times 442016 (25.93%) aligned exactly 1 time 153524 (9.01%) aligned >1 times 96.98% overall alignment rate Time searching: 00:22:55 Overall time: 00:22:55 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] 799184 / 17430146 = 0.0459 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 08:06:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.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 08:06:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:06:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:06:09: 1000000 INFO @ Tue, 14 Jul 2020 08:06:17: 2000000 INFO @ Tue, 14 Jul 2020 08:06:24: 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 08:06:32: 4000000 INFO @ Tue, 14 Jul 2020 08:06:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.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 08:06:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:06:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:06:39: 5000000 INFO @ Tue, 14 Jul 2020 08:06:40: 1000000 INFO @ Tue, 14 Jul 2020 08:06:47: 6000000 INFO @ Tue, 14 Jul 2020 08:06:48: 2000000 INFO @ Tue, 14 Jul 2020 08:06:54: 7000000 INFO @ Tue, 14 Jul 2020 08:06:56: 3000000 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 08:07:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.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 08:07:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:07:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:07:02: 8000000 INFO @ Tue, 14 Jul 2020 08:07:05: 4000000 INFO @ Tue, 14 Jul 2020 08:07:10: 9000000 INFO @ Tue, 14 Jul 2020 08:07:10: 1000000 INFO @ Tue, 14 Jul 2020 08:07:13: 5000000 INFO @ Tue, 14 Jul 2020 08:07:17: 10000000 INFO @ Tue, 14 Jul 2020 08:07:19: 2000000 INFO @ Tue, 14 Jul 2020 08:07:21: 6000000 INFO @ Tue, 14 Jul 2020 08:07:26: 11000000 INFO @ Tue, 14 Jul 2020 08:07:27: 3000000 INFO @ Tue, 14 Jul 2020 08:07:28: 7000000 INFO @ Tue, 14 Jul 2020 08:07:34: 12000000 INFO @ Tue, 14 Jul 2020 08:07:35: 4000000 INFO @ Tue, 14 Jul 2020 08:07:36: 8000000 INFO @ Tue, 14 Jul 2020 08:07:42: 13000000 INFO @ Tue, 14 Jul 2020 08:07:43: 9000000 INFO @ Tue, 14 Jul 2020 08:07:43: 5000000 INFO @ Tue, 14 Jul 2020 08:07:49: 14000000 INFO @ Tue, 14 Jul 2020 08:07:51: 10000000 INFO @ Tue, 14 Jul 2020 08:07:52: 6000000 INFO @ Tue, 14 Jul 2020 08:07:57: 15000000 INFO @ Tue, 14 Jul 2020 08:07:59: 7000000 INFO @ Tue, 14 Jul 2020 08:07:59: 11000000 INFO @ Tue, 14 Jul 2020 08:08:05: 16000000 INFO @ Tue, 14 Jul 2020 08:08:07: 8000000 INFO @ Tue, 14 Jul 2020 08:08:07: 12000000 INFO @ Tue, 14 Jul 2020 08:08:12: 17000000 INFO @ Tue, 14 Jul 2020 08:08:14: 9000000 INFO @ Tue, 14 Jul 2020 08:08:16: 13000000 INFO @ Tue, 14 Jul 2020 08:08:20: 18000000 INFO @ Tue, 14 Jul 2020 08:08:22: 10000000 INFO @ Tue, 14 Jul 2020 08:08:23: 14000000 INFO @ Tue, 14 Jul 2020 08:08:27: 19000000 INFO @ Tue, 14 Jul 2020 08:08:30: 11000000 INFO @ Tue, 14 Jul 2020 08:08:31: 15000000 INFO @ Tue, 14 Jul 2020 08:08:35: 20000000 INFO @ Tue, 14 Jul 2020 08:08:38: 12000000 INFO @ Tue, 14 Jul 2020 08:08:39: 16000000 INFO @ Tue, 14 Jul 2020 08:08:42: 21000000 INFO @ Tue, 14 Jul 2020 08:08:46: 13000000 INFO @ Tue, 14 Jul 2020 08:08:47: 17000000 INFO @ Tue, 14 Jul 2020 08:08:50: 22000000 INFO @ Tue, 14 Jul 2020 08:08:54: 18000000 INFO @ Tue, 14 Jul 2020 08:08:54: 14000000 INFO @ Tue, 14 Jul 2020 08:08:57: 23000000 INFO @ Tue, 14 Jul 2020 08:09:02: 19000000 INFO @ Tue, 14 Jul 2020 08:09:02: 15000000 INFO @ Tue, 14 Jul 2020 08:09:05: 24000000 INFO @ Tue, 14 Jul 2020 08:09:10: 20000000 INFO @ Tue, 14 Jul 2020 08:09:10: 16000000 INFO @ Tue, 14 Jul 2020 08:09:12: 25000000 INFO @ Tue, 14 Jul 2020 08:09:17: 21000000 INFO @ Tue, 14 Jul 2020 08:09:18: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:09:20: 26000000 INFO @ Tue, 14 Jul 2020 08:09:25: 22000000 INFO @ Tue, 14 Jul 2020 08:09:26: 18000000 INFO @ Tue, 14 Jul 2020 08:09:28: 27000000 INFO @ Tue, 14 Jul 2020 08:09:32: 23000000 INFO @ Tue, 14 Jul 2020 08:09:34: 19000000 INFO @ Tue, 14 Jul 2020 08:09:35: 28000000 INFO @ Tue, 14 Jul 2020 08:09:40: 24000000 INFO @ Tue, 14 Jul 2020 08:09:41: 20000000 INFO @ Tue, 14 Jul 2020 08:09:43: 29000000 INFO @ Tue, 14 Jul 2020 08:09:48: 25000000 INFO @ Tue, 14 Jul 2020 08:09:49: 21000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:09:51: 30000000 INFO @ Tue, 14 Jul 2020 08:09:55: 26000000 INFO @ Tue, 14 Jul 2020 08:09:57: 22000000 INFO @ Tue, 14 Jul 2020 08:09:58: 31000000 INFO @ Tue, 14 Jul 2020 08:10:03: 27000000 INFO @ Tue, 14 Jul 2020 08:10:06: 23000000 INFO @ Tue, 14 Jul 2020 08:10:06: 32000000 INFO @ Tue, 14 Jul 2020 08:10:10: 28000000 INFO @ Tue, 14 Jul 2020 08:10:13: 33000000 INFO @ Tue, 14 Jul 2020 08:10:14: 24000000 INFO @ Tue, 14 Jul 2020 08:10:18: 29000000 INFO @ Tue, 14 Jul 2020 08:10:21: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:10:21: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:10:21: #1 total tags in treatment: 16598567 INFO @ Tue, 14 Jul 2020 08:10:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:10:21: #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 08:10:21: #1 tags after filtering in treatment: 12162446 INFO @ Tue, 14 Jul 2020 08:10:21: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 14 Jul 2020 08:10:21: #1 finished! INFO @ Tue, 14 Jul 2020 08:10:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:10:21: 25000000 INFO @ Tue, 14 Jul 2020 08:10:23: #2 number of paired peaks: 14243 INFO @ Tue, 14 Jul 2020 08:10:23: start model_add_line... INFO @ Tue, 14 Jul 2020 08:10:23: start X-correlation... INFO @ Tue, 14 Jul 2020 08:10:23: end of X-cor INFO @ Tue, 14 Jul 2020 08:10:23: #2 finished! INFO @ Tue, 14 Jul 2020 08:10:23: #2 predicted fragment length is 143 bps INFO @ Tue, 14 Jul 2020 08:10:23: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 14 Jul 2020 08:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.05_model.r WARNING @ Tue, 14 Jul 2020 08:10:23: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:10:23: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 14 Jul 2020 08:10:23: #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 08:10:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:10:26: 30000000 INFO @ Tue, 14 Jul 2020 08:10:29: 26000000 INFO @ Tue, 14 Jul 2020 08:10:34: 31000000 INFO @ Tue, 14 Jul 2020 08:10:37: 27000000 INFO @ Tue, 14 Jul 2020 08:10:42: 32000000 INFO @ Tue, 14 Jul 2020 08:10:45: 28000000 INFO @ Tue, 14 Jul 2020 08:10:49: 33000000 INFO @ Tue, 14 Jul 2020 08:10:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:10:53: 29000000 INFO @ Tue, 14 Jul 2020 08:10:57: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:10:57: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:10:57: #1 total tags in treatment: 16598567 INFO @ Tue, 14 Jul 2020 08:10:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:10:57: #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 08:10:57: #1 tags after filtering in treatment: 12162446 INFO @ Tue, 14 Jul 2020 08:10:57: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 14 Jul 2020 08:10:57: #1 finished! INFO @ Tue, 14 Jul 2020 08:10:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:10:59: #2 number of paired peaks: 14243 INFO @ Tue, 14 Jul 2020 08:10:59: start model_add_line... INFO @ Tue, 14 Jul 2020 08:10:59: start X-correlation... INFO @ Tue, 14 Jul 2020 08:10:59: end of X-cor INFO @ Tue, 14 Jul 2020 08:10:59: #2 finished! INFO @ Tue, 14 Jul 2020 08:10:59: #2 predicted fragment length is 143 bps INFO @ Tue, 14 Jul 2020 08:10:59: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 14 Jul 2020 08:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.10_model.r WARNING @ Tue, 14 Jul 2020 08:10:59: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:10:59: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 14 Jul 2020 08:10:59: #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 08:10:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:11:00: 30000000 INFO @ Tue, 14 Jul 2020 08:11:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:11:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:11:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.05_summits.bed INFO @ Tue, 14 Jul 2020 08:11:05: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8849 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:11:07: 31000000 INFO @ Tue, 14 Jul 2020 08:11:14: 32000000 INFO @ Tue, 14 Jul 2020 08:11:21: 33000000 INFO @ Tue, 14 Jul 2020 08:11:28: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:11:28: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:11:28: #1 total tags in treatment: 16598567 INFO @ Tue, 14 Jul 2020 08:11:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:11:28: #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 08:11:28: #1 tags after filtering in treatment: 12162446 INFO @ Tue, 14 Jul 2020 08:11:28: #1 Redundant rate of treatment: 0.27 INFO @ Tue, 14 Jul 2020 08:11:28: #1 finished! INFO @ Tue, 14 Jul 2020 08:11:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:11:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:11:30: #2 number of paired peaks: 14243 INFO @ Tue, 14 Jul 2020 08:11:30: start model_add_line... INFO @ Tue, 14 Jul 2020 08:11:30: start X-correlation... INFO @ Tue, 14 Jul 2020 08:11:30: end of X-cor INFO @ Tue, 14 Jul 2020 08:11:30: #2 finished! INFO @ Tue, 14 Jul 2020 08:11:30: #2 predicted fragment length is 143 bps INFO @ Tue, 14 Jul 2020 08:11:30: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 14 Jul 2020 08:11:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.20_model.r WARNING @ Tue, 14 Jul 2020 08:11:30: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:11:30: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 14 Jul 2020 08:11:30: #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 08:11:30: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:11:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.10_summits.bed INFO @ Tue, 14 Jul 2020 08:11:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (8295 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:11:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224530/SRX7224530.20_summits.bed INFO @ Tue, 14 Jul 2020 08:12:12: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7332 records, 4 fields): 8 millis CompletedMACS2peakCalling