Job ID = 12265369 SRX = SRX6817528 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 33094297 spots for SRR10084519/SRR10084519.sra Written 33094297 spots for SRR10084519/SRR10084519.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265967 ("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: 01:40:08 33094297 reads; of these: 33094297 (100.00%) were paired; of these: 16345660 (49.39%) aligned concordantly 0 times 10672006 (32.25%) aligned concordantly exactly 1 time 6076631 (18.36%) aligned concordantly >1 times ---- 16345660 pairs aligned concordantly 0 times; of these: 3471297 (21.24%) aligned discordantly 1 time ---- 12874363 pairs aligned 0 times concordantly or discordantly; of these: 25748726 mates make up the pairs; of these: 20616778 (80.07%) aligned 0 times 1255721 (4.88%) aligned exactly 1 time 3876227 (15.05%) aligned >1 times 68.85% overall alignment rate Time searching: 01:40:08 Overall time: 01:40:08 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] 6831771 / 20104055 = 0.3398 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:52:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.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, 03 Apr 2021 08:52:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:52:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:52:56: 1000000 INFO @ Sat, 03 Apr 2021 08:53:03: 2000000 INFO @ Sat, 03 Apr 2021 08:53:10: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:53:17: 4000000 INFO @ Sat, 03 Apr 2021 08:53:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.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, 03 Apr 2021 08:53:18: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:53:18: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:53:25: 5000000 INFO @ Sat, 03 Apr 2021 08:53:26: 1000000 INFO @ Sat, 03 Apr 2021 08:53:33: 6000000 INFO @ Sat, 03 Apr 2021 08:53:34: 2000000 INFO @ Sat, 03 Apr 2021 08:53:41: 7000000 INFO @ Sat, 03 Apr 2021 08:53:43: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 08:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.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, 03 Apr 2021 08:53:48: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:53:48: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:53:49: 8000000 INFO @ Sat, 03 Apr 2021 08:53:51: 4000000 INFO @ Sat, 03 Apr 2021 08:53:57: 9000000 INFO @ Sat, 03 Apr 2021 08:53:57: 1000000 INFO @ Sat, 03 Apr 2021 08:53:59: 5000000 INFO @ Sat, 03 Apr 2021 08:54:05: 10000000 INFO @ Sat, 03 Apr 2021 08:54:06: 2000000 INFO @ Sat, 03 Apr 2021 08:54:07: 6000000 INFO @ Sat, 03 Apr 2021 08:54:14: 11000000 INFO @ Sat, 03 Apr 2021 08:54:15: 7000000 INFO @ Sat, 03 Apr 2021 08:54:15: 3000000 INFO @ Sat, 03 Apr 2021 08:54:22: 12000000 INFO @ Sat, 03 Apr 2021 08:54:24: 8000000 INFO @ Sat, 03 Apr 2021 08:54:24: 4000000 INFO @ Sat, 03 Apr 2021 08:54:30: 13000000 INFO @ Sat, 03 Apr 2021 08:54:32: 9000000 INFO @ Sat, 03 Apr 2021 08:54:33: 5000000 INFO @ Sat, 03 Apr 2021 08:54:38: 14000000 INFO @ Sat, 03 Apr 2021 08:54:40: 10000000 INFO @ Sat, 03 Apr 2021 08:54:42: 6000000 INFO @ Sat, 03 Apr 2021 08:54:46: 15000000 INFO @ Sat, 03 Apr 2021 08:54:49: 11000000 INFO @ Sat, 03 Apr 2021 08:54:51: 7000000 INFO @ Sat, 03 Apr 2021 08:54:54: 16000000 INFO @ Sat, 03 Apr 2021 08:54:57: 12000000 INFO @ Sat, 03 Apr 2021 08:55:00: 8000000 INFO @ Sat, 03 Apr 2021 08:55:02: 17000000 INFO @ Sat, 03 Apr 2021 08:55:05: 13000000 INFO @ Sat, 03 Apr 2021 08:55:09: 9000000 INFO @ Sat, 03 Apr 2021 08:55:10: 18000000 INFO @ Sat, 03 Apr 2021 08:55:13: 14000000 INFO @ Sat, 03 Apr 2021 08:55:18: 19000000 INFO @ Sat, 03 Apr 2021 08:55:18: 10000000 INFO @ Sat, 03 Apr 2021 08:55:21: 15000000 INFO @ Sat, 03 Apr 2021 08:55:26: 20000000 INFO @ Sat, 03 Apr 2021 08:55:27: 11000000 INFO @ Sat, 03 Apr 2021 08:55:29: 16000000 INFO @ Sat, 03 Apr 2021 08:55:34: 21000000 INFO @ Sat, 03 Apr 2021 08:55:37: 12000000 INFO @ Sat, 03 Apr 2021 08:55:37: 17000000 INFO @ Sat, 03 Apr 2021 08:55:41: 22000000 INFO @ Sat, 03 Apr 2021 08:55:45: 18000000 INFO @ Sat, 03 Apr 2021 08:55:46: 13000000 INFO @ Sat, 03 Apr 2021 08:55:49: 23000000 INFO @ Sat, 03 Apr 2021 08:55:53: 19000000 INFO @ Sat, 03 Apr 2021 08:55:54: 14000000 INFO @ Sat, 03 Apr 2021 08:55:57: 24000000 INFO @ Sat, 03 Apr 2021 08:56:01: 20000000 INFO @ Sat, 03 Apr 2021 08:56:03: 15000000 INFO @ Sat, 03 Apr 2021 08:56:05: 25000000 INFO @ Sat, 03 Apr 2021 08:56:09: 21000000 INFO @ Sat, 03 Apr 2021 08:56:12: 16000000 INFO @ Sat, 03 Apr 2021 08:56:14: 26000000 INFO @ Sat, 03 Apr 2021 08:56:16: 22000000 INFO @ Sat, 03 Apr 2021 08:56:21: 17000000 INFO @ Sat, 03 Apr 2021 08:56:22: 27000000 INFO @ Sat, 03 Apr 2021 08:56:24: 23000000 INFO @ Sat, 03 Apr 2021 08:56:30: 18000000 INFO @ Sat, 03 Apr 2021 08:56:30: 28000000 INFO @ Sat, 03 Apr 2021 08:56:32: 24000000 INFO @ Sat, 03 Apr 2021 08:56:38: 29000000 INFO @ Sat, 03 Apr 2021 08:56:38: 19000000 INFO @ Sat, 03 Apr 2021 08:56:40: 25000000 INFO @ Sat, 03 Apr 2021 08:56:47: 30000000 INFO @ Sat, 03 Apr 2021 08:56:47: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:56:48: 26000000 INFO @ Sat, 03 Apr 2021 08:56:55: 31000000 INFO @ Sat, 03 Apr 2021 08:56:56: 21000000 INFO @ Sat, 03 Apr 2021 08:56:57: 27000000 INFO @ Sat, 03 Apr 2021 08:57:03: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:57:03: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:57:03: #1 total tags in treatment: 10688472 INFO @ Sat, 03 Apr 2021 08:57:03: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:57:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:57:03: #1 tags after filtering in treatment: 8712766 INFO @ Sat, 03 Apr 2021 08:57:03: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:57:03: #1 finished! INFO @ Sat, 03 Apr 2021 08:57:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:57:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:57:03: #2 number of paired peaks: 394 WARNING @ Sat, 03 Apr 2021 08:57:03: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 03 Apr 2021 08:57:03: start model_add_line... INFO @ Sat, 03 Apr 2021 08:57:03: start X-correlation... INFO @ Sat, 03 Apr 2021 08:57:03: end of X-cor INFO @ Sat, 03 Apr 2021 08:57:03: #2 finished! INFO @ Sat, 03 Apr 2021 08:57:03: #2 predicted fragment length is 199 bps INFO @ Sat, 03 Apr 2021 08:57:03: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 03 Apr 2021 08:57:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.05_model.r WARNING @ Sat, 03 Apr 2021 08:57:03: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:57:03: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 03 Apr 2021 08:57:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:57:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:57:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:57:04: 22000000 INFO @ Sat, 03 Apr 2021 08:57:05: 28000000 INFO @ Sat, 03 Apr 2021 08:57:13: 23000000 INFO @ Sat, 03 Apr 2021 08:57:14: 29000000 INFO @ Sat, 03 Apr 2021 08:57:22: 24000000 INFO @ Sat, 03 Apr 2021 08:57:22: 30000000 INFO @ Sat, 03 Apr 2021 08:57:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:57:30: 31000000 INFO @ Sat, 03 Apr 2021 08:57:30: 25000000 INFO @ Sat, 03 Apr 2021 08:57:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.05_summits.bed INFO @ Sat, 03 Apr 2021 08:57:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3986 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:57:38: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:57:38: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:57:38: #1 total tags in treatment: 10688472 INFO @ Sat, 03 Apr 2021 08:57:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:57:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:57:38: #1 tags after filtering in treatment: 8712766 INFO @ Sat, 03 Apr 2021 08:57:38: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:57:38: #1 finished! INFO @ Sat, 03 Apr 2021 08:57:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:57:39: #2 number of paired peaks: 394 WARNING @ Sat, 03 Apr 2021 08:57:39: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 03 Apr 2021 08:57:39: start model_add_line... INFO @ Sat, 03 Apr 2021 08:57:39: start X-correlation... INFO @ Sat, 03 Apr 2021 08:57:39: end of X-cor INFO @ Sat, 03 Apr 2021 08:57:39: #2 finished! INFO @ Sat, 03 Apr 2021 08:57:39: #2 predicted fragment length is 199 bps INFO @ Sat, 03 Apr 2021 08:57:39: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 03 Apr 2021 08:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.10_model.r WARNING @ Sat, 03 Apr 2021 08:57:39: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:57:39: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 03 Apr 2021 08:57:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:57:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:57:39: 26000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:57:48: 27000000 INFO @ Sat, 03 Apr 2021 08:57:57: 28000000 INFO @ Sat, 03 Apr 2021 08:57:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:58:06: 29000000 INFO @ Sat, 03 Apr 2021 08:58:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:58:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:58:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.10_summits.bed INFO @ Sat, 03 Apr 2021 08:58:09: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1743 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:58:15: 30000000 INFO @ Sat, 03 Apr 2021 08:58:23: 31000000 INFO @ Sat, 03 Apr 2021 08:58:32: #1 tag size is determined as 150 bps INFO @ Sat, 03 Apr 2021 08:58:32: #1 tag size = 150 INFO @ Sat, 03 Apr 2021 08:58:32: #1 total tags in treatment: 10688472 INFO @ Sat, 03 Apr 2021 08:58:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:58:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 08:58:32: #1 tags after filtering in treatment: 8712766 INFO @ Sat, 03 Apr 2021 08:58:32: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 08:58:32: #1 finished! INFO @ Sat, 03 Apr 2021 08:58:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:58:32: #2 number of paired peaks: 394 WARNING @ Sat, 03 Apr 2021 08:58:32: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Sat, 03 Apr 2021 08:58:32: start model_add_line... INFO @ Sat, 03 Apr 2021 08:58:33: start X-correlation... INFO @ Sat, 03 Apr 2021 08:58:33: end of X-cor INFO @ Sat, 03 Apr 2021 08:58:33: #2 finished! INFO @ Sat, 03 Apr 2021 08:58:33: #2 predicted fragment length is 199 bps INFO @ Sat, 03 Apr 2021 08:58:33: #2 alternative fragment length(s) may be 199 bps INFO @ Sat, 03 Apr 2021 08:58:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.20_model.r WARNING @ Sat, 03 Apr 2021 08:58:33: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:58:33: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Sat, 03 Apr 2021 08:58:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 08:58:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:58:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:59:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:59:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:59:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6817528/SRX6817528.20_summits.bed INFO @ Sat, 03 Apr 2021 08:59:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 2 millis CompletedMACS2peakCalling