Job ID = 12265568 SRX = SRX7277027 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26226598 spots for SRR10597292/SRR10597292.sra Written 26226598 spots for SRR10597292/SRR10597292.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265957 ("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: 00:51:24 26226598 reads; of these: 26226598 (100.00%) were paired; of these: 9972161 (38.02%) aligned concordantly 0 times 11392786 (43.44%) aligned concordantly exactly 1 time 4861651 (18.54%) aligned concordantly >1 times ---- 9972161 pairs aligned concordantly 0 times; of these: 2692233 (27.00%) aligned discordantly 1 time ---- 7279928 pairs aligned 0 times concordantly or discordantly; of these: 14559856 mates make up the pairs; of these: 11846374 (81.36%) aligned 0 times 775909 (5.33%) aligned exactly 1 time 1937573 (13.31%) aligned >1 times 77.42% overall alignment rate Time searching: 00:51:24 Overall time: 00:51:24 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 20 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] 2975269 / 18809568 = 0.1582 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 08:52:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.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 08:52:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:52:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:53:07: 1000000 INFO @ Sat, 03 Apr 2021 08:53:18: 2000000 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 08:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.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 08:53:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:53:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:53:28: 3000000 INFO @ Sat, 03 Apr 2021 08:53:37: 1000000 INFO @ Sat, 03 Apr 2021 08:53:39: 4000000 INFO @ Sat, 03 Apr 2021 08:53:47: 2000000 INFO @ Sat, 03 Apr 2021 08:53:49: 5000000 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 08:53:56: 3000000 INFO @ Sat, 03 Apr 2021 08:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.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 08:53:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:53:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:54:01: 6000000 INFO @ Sat, 03 Apr 2021 08:54:06: 4000000 INFO @ Sat, 03 Apr 2021 08:54:08: 1000000 INFO @ Sat, 03 Apr 2021 08:54:12: 7000000 INFO @ Sat, 03 Apr 2021 08:54:16: 5000000 INFO @ Sat, 03 Apr 2021 08:54:20: 2000000 INFO @ Sat, 03 Apr 2021 08:54:23: 8000000 INFO @ Sat, 03 Apr 2021 08:54:26: 6000000 INFO @ Sat, 03 Apr 2021 08:54:31: 3000000 INFO @ Sat, 03 Apr 2021 08:54:35: 9000000 INFO @ Sat, 03 Apr 2021 08:54:36: 7000000 INFO @ Sat, 03 Apr 2021 08:54:43: 4000000 INFO @ Sat, 03 Apr 2021 08:54:46: 8000000 INFO @ Sat, 03 Apr 2021 08:54:47: 10000000 INFO @ Sat, 03 Apr 2021 08:54:55: 5000000 INFO @ Sat, 03 Apr 2021 08:54:57: 9000000 INFO @ Sat, 03 Apr 2021 08:54:58: 11000000 INFO @ Sat, 03 Apr 2021 08:55:06: 6000000 INFO @ Sat, 03 Apr 2021 08:55:08: 10000000 INFO @ Sat, 03 Apr 2021 08:55:10: 12000000 INFO @ Sat, 03 Apr 2021 08:55:18: 7000000 INFO @ Sat, 03 Apr 2021 08:55:20: 11000000 INFO @ Sat, 03 Apr 2021 08:55:22: 13000000 INFO @ Sat, 03 Apr 2021 08:55:30: 8000000 INFO @ Sat, 03 Apr 2021 08:55:32: 12000000 INFO @ Sat, 03 Apr 2021 08:55:33: 14000000 INFO @ Sat, 03 Apr 2021 08:55:42: 9000000 INFO @ Sat, 03 Apr 2021 08:55:44: 13000000 INFO @ Sat, 03 Apr 2021 08:55:46: 15000000 INFO @ Sat, 03 Apr 2021 08:55:54: 10000000 INFO @ Sat, 03 Apr 2021 08:55:55: 14000000 INFO @ Sat, 03 Apr 2021 08:55:57: 16000000 INFO @ Sat, 03 Apr 2021 08:56:06: 11000000 INFO @ Sat, 03 Apr 2021 08:56:08: 15000000 INFO @ Sat, 03 Apr 2021 08:56:10: 17000000 INFO @ Sat, 03 Apr 2021 08:56:19: 12000000 INFO @ Sat, 03 Apr 2021 08:56:19: 16000000 INFO @ Sat, 03 Apr 2021 08:56:22: 18000000 INFO @ Sat, 03 Apr 2021 08:56:31: 13000000 INFO @ Sat, 03 Apr 2021 08:56:31: 17000000 INFO @ Sat, 03 Apr 2021 08:56:34: 19000000 INFO @ Sat, 03 Apr 2021 08:56:43: 14000000 INFO @ Sat, 03 Apr 2021 08:56:43: 18000000 INFO @ Sat, 03 Apr 2021 08:56:46: 20000000 INFO @ Sat, 03 Apr 2021 08:56:54: 15000000 INFO @ Sat, 03 Apr 2021 08:56:55: 19000000 INFO @ Sat, 03 Apr 2021 08:56:57: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:57:05: 16000000 INFO @ Sat, 03 Apr 2021 08:57:07: 20000000 INFO @ Sat, 03 Apr 2021 08:57:09: 22000000 INFO @ Sat, 03 Apr 2021 08:57:17: 17000000 INFO @ Sat, 03 Apr 2021 08:57:19: 21000000 INFO @ Sat, 03 Apr 2021 08:57:20: 23000000 INFO @ Sat, 03 Apr 2021 08:57:28: 18000000 INFO @ Sat, 03 Apr 2021 08:57:31: 22000000 INFO @ Sat, 03 Apr 2021 08:57:32: 24000000 INFO @ Sat, 03 Apr 2021 08:57:40: 19000000 INFO @ Sat, 03 Apr 2021 08:57:43: 23000000 INFO @ Sat, 03 Apr 2021 08:57:44: 25000000 INFO @ Sat, 03 Apr 2021 08:57:52: 20000000 INFO @ Sat, 03 Apr 2021 08:57:55: 24000000 INFO @ Sat, 03 Apr 2021 08:57:55: 26000000 INFO @ Sat, 03 Apr 2021 08:58:03: 21000000 INFO @ Sat, 03 Apr 2021 08:58:07: 25000000 INFO @ Sat, 03 Apr 2021 08:58:07: 27000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:58:15: 22000000 INFO @ Sat, 03 Apr 2021 08:58:19: 28000000 INFO @ Sat, 03 Apr 2021 08:58:19: 26000000 INFO @ Sat, 03 Apr 2021 08:58:27: 23000000 INFO @ Sat, 03 Apr 2021 08:58:31: 29000000 INFO @ Sat, 03 Apr 2021 08:58:31: 27000000 INFO @ Sat, 03 Apr 2021 08:58:38: 24000000 INFO @ Sat, 03 Apr 2021 08:58:42: 30000000 INFO @ Sat, 03 Apr 2021 08:58:43: 28000000 INFO @ Sat, 03 Apr 2021 08:58:50: 25000000 INFO @ Sat, 03 Apr 2021 08:58:54: 31000000 INFO @ Sat, 03 Apr 2021 08:58:55: 29000000 INFO @ Sat, 03 Apr 2021 08:59:02: 26000000 INFO @ Sat, 03 Apr 2021 08:59:05: 32000000 INFO @ Sat, 03 Apr 2021 08:59:05: 30000000 INFO @ Sat, 03 Apr 2021 08:59:13: 27000000 INFO @ Sat, 03 Apr 2021 08:59:16: 33000000 INFO @ Sat, 03 Apr 2021 08:59:16: 31000000 INFO @ Sat, 03 Apr 2021 08:59:24: 28000000 INFO @ Sat, 03 Apr 2021 08:59:26: 32000000 INFO @ Sat, 03 Apr 2021 08:59:26: 34000000 INFO @ Sat, 03 Apr 2021 08:59:33: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:59:33: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:59:33: #1 total tags in treatment: 13419315 INFO @ Sat, 03 Apr 2021 08:59:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:59:33: #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 08:59:34: #1 tags after filtering in treatment: 10662844 INFO @ Sat, 03 Apr 2021 08:59:34: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:59:34: #1 finished! INFO @ Sat, 03 Apr 2021 08:59:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:59:34: #2 number of paired peaks: 254 WARNING @ Sat, 03 Apr 2021 08:59:34: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sat, 03 Apr 2021 08:59:34: start model_add_line... INFO @ Sat, 03 Apr 2021 08:59:35: start X-correlation... INFO @ Sat, 03 Apr 2021 08:59:35: end of X-cor INFO @ Sat, 03 Apr 2021 08:59:35: #2 finished! INFO @ Sat, 03 Apr 2021 08:59:35: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 08:59:35: #2 alternative fragment length(s) may be 4,99,581 bps INFO @ Sat, 03 Apr 2021 08:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.05_model.r WARNING @ Sat, 03 Apr 2021 08:59:35: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:59:35: #2 You may need to consider one of the other alternative d(s): 4,99,581 WARNING @ Sat, 03 Apr 2021 08:59:35: #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 08:59:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:59:35: 29000000 INFO @ Sat, 03 Apr 2021 08:59:37: 33000000 INFO @ Sat, 03 Apr 2021 08:59:45: 30000000 INFO @ Sat, 03 Apr 2021 08:59:47: 34000000 INFO @ Sat, 03 Apr 2021 08:59:52: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:59:52: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:59:52: #1 total tags in treatment: 13419315 INFO @ Sat, 03 Apr 2021 08:59:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:59:52: #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 08:59:52: #1 tags after filtering in treatment: 10662844 INFO @ Sat, 03 Apr 2021 08:59:52: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:59:52: #1 finished! INFO @ Sat, 03 Apr 2021 08:59:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:59:53: #2 number of paired peaks: 254 WARNING @ Sat, 03 Apr 2021 08:59:53: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sat, 03 Apr 2021 08:59:53: start model_add_line... INFO @ Sat, 03 Apr 2021 08:59:53: start X-correlation... INFO @ Sat, 03 Apr 2021 08:59:53: end of X-cor INFO @ Sat, 03 Apr 2021 08:59:53: #2 finished! INFO @ Sat, 03 Apr 2021 08:59:53: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 08:59:53: #2 alternative fragment length(s) may be 4,99,581 bps INFO @ Sat, 03 Apr 2021 08:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.10_model.r WARNING @ Sat, 03 Apr 2021 08:59:53: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:59:53: #2 You may need to consider one of the other alternative d(s): 4,99,581 WARNING @ Sat, 03 Apr 2021 08:59:53: #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 08:59:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:59:56: 31000000 INFO @ Sat, 03 Apr 2021 08:59:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:00:06: 32000000 INFO @ Sat, 03 Apr 2021 09:00:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:00:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:00:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.05_summits.bed INFO @ Sat, 03 Apr 2021 09:00:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6919 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:00:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:00:15: 33000000 INFO @ Sat, 03 Apr 2021 09:00:23: 34000000 INFO @ Sat, 03 Apr 2021 09:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.10_summits.bed INFO @ Sat, 03 Apr 2021 09:00:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1959 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:00:28: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 09:00:28: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 09:00:28: #1 total tags in treatment: 13419315 INFO @ Sat, 03 Apr 2021 09:00:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:00:28: #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 09:00:29: #1 tags after filtering in treatment: 10662844 INFO @ Sat, 03 Apr 2021 09:00:29: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 09:00:29: #1 finished! INFO @ Sat, 03 Apr 2021 09:00:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:00:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:00:29: #2 number of paired peaks: 254 WARNING @ Sat, 03 Apr 2021 09:00:29: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sat, 03 Apr 2021 09:00:29: start model_add_line... INFO @ Sat, 03 Apr 2021 09:00:30: start X-correlation... INFO @ Sat, 03 Apr 2021 09:00:30: end of X-cor INFO @ Sat, 03 Apr 2021 09:00:30: #2 finished! INFO @ Sat, 03 Apr 2021 09:00:30: #2 predicted fragment length is 99 bps INFO @ Sat, 03 Apr 2021 09:00:30: #2 alternative fragment length(s) may be 4,99,581 bps INFO @ Sat, 03 Apr 2021 09:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.20_model.r WARNING @ Sat, 03 Apr 2021 09:00:30: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:00:30: #2 You may need to consider one of the other alternative d(s): 4,99,581 WARNING @ Sat, 03 Apr 2021 09:00:30: #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 09:00:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:00:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:00:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277027/SRX7277027.20_summits.bed INFO @ Sat, 03 Apr 2021 09:01:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling