Job ID = 12265599 SRX = SRX7277032 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25678673 spots for SRR10597297/SRR10597297.sra Written 25678673 spots for SRR10597297/SRR10597297.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265941 ("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: 00:41:55 25678673 reads; of these: 25678673 (100.00%) were paired; of these: 10022917 (39.03%) aligned concordantly 0 times 9856667 (38.38%) aligned concordantly exactly 1 time 5799089 (22.58%) aligned concordantly >1 times ---- 10022917 pairs aligned concordantly 0 times; of these: 2390464 (23.85%) aligned discordantly 1 time ---- 7632453 pairs aligned 0 times concordantly or discordantly; of these: 15264906 mates make up the pairs; of these: 12144259 (79.56%) aligned 0 times 711051 (4.66%) aligned exactly 1 time 2409596 (15.79%) aligned >1 times 76.35% overall alignment rate Time searching: 00:41:55 Overall time: 00:41:55 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] 3533670 / 17899681 = 0.1974 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 08:46:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.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 08:46:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:46:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:46:27: 1000000 INFO @ Sat, 03 Apr 2021 08:46:33: 2000000 INFO @ Sat, 03 Apr 2021 08:46:39: 3000000 INFO @ Sat, 03 Apr 2021 08:46:45: 4000000 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 08:46:51: 5000000 INFO @ Sat, 03 Apr 2021 08:46:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.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 08:46:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:46:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:46:58: 6000000 INFO @ Sat, 03 Apr 2021 08:46:59: 1000000 INFO @ Sat, 03 Apr 2021 08:47:04: 7000000 INFO @ Sat, 03 Apr 2021 08:47:06: 2000000 INFO @ Sat, 03 Apr 2021 08:47:11: 8000000 INFO @ Sat, 03 Apr 2021 08:47:14: 3000000 INFO @ Sat, 03 Apr 2021 08:47:18: 9000000 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 08:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.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 08:47:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:47:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:47:21: 4000000 INFO @ Sat, 03 Apr 2021 08:47:24: 10000000 INFO @ Sat, 03 Apr 2021 08:47:29: 1000000 INFO @ Sat, 03 Apr 2021 08:47:29: 5000000 INFO @ Sat, 03 Apr 2021 08:47:31: 11000000 INFO @ Sat, 03 Apr 2021 08:47:36: 2000000 INFO @ Sat, 03 Apr 2021 08:47:37: 6000000 INFO @ Sat, 03 Apr 2021 08:47:38: 12000000 INFO @ Sat, 03 Apr 2021 08:47:44: 3000000 INFO @ Sat, 03 Apr 2021 08:47:44: 7000000 INFO @ Sat, 03 Apr 2021 08:47:45: 13000000 INFO @ Sat, 03 Apr 2021 08:47:51: 4000000 INFO @ Sat, 03 Apr 2021 08:47:52: 8000000 INFO @ Sat, 03 Apr 2021 08:47:52: 14000000 INFO @ Sat, 03 Apr 2021 08:47:58: 5000000 INFO @ Sat, 03 Apr 2021 08:47:59: 15000000 INFO @ Sat, 03 Apr 2021 08:47:59: 9000000 INFO @ Sat, 03 Apr 2021 08:48:06: 6000000 INFO @ Sat, 03 Apr 2021 08:48:06: 16000000 INFO @ Sat, 03 Apr 2021 08:48:07: 10000000 INFO @ Sat, 03 Apr 2021 08:48:13: 17000000 INFO @ Sat, 03 Apr 2021 08:48:13: 7000000 INFO @ Sat, 03 Apr 2021 08:48:15: 11000000 INFO @ Sat, 03 Apr 2021 08:48:20: 18000000 INFO @ Sat, 03 Apr 2021 08:48:21: 8000000 INFO @ Sat, 03 Apr 2021 08:48:22: 12000000 INFO @ Sat, 03 Apr 2021 08:48:27: 19000000 INFO @ Sat, 03 Apr 2021 08:48:29: 9000000 INFO @ Sat, 03 Apr 2021 08:48:30: 13000000 INFO @ Sat, 03 Apr 2021 08:48:34: 20000000 INFO @ Sat, 03 Apr 2021 08:48:37: 14000000 INFO @ Sat, 03 Apr 2021 08:48:38: 10000000 INFO @ Sat, 03 Apr 2021 08:48:40: 21000000 INFO @ Sat, 03 Apr 2021 08:48:45: 15000000 INFO @ Sat, 03 Apr 2021 08:48:46: 11000000 INFO @ Sat, 03 Apr 2021 08:48:47: 22000000 INFO @ Sat, 03 Apr 2021 08:48:52: 16000000 INFO @ Sat, 03 Apr 2021 08:48:54: 23000000 INFO @ Sat, 03 Apr 2021 08:48:55: 12000000 INFO @ Sat, 03 Apr 2021 08:49:00: 17000000 INFO @ Sat, 03 Apr 2021 08:49:00: 24000000 INFO @ Sat, 03 Apr 2021 08:49:03: 13000000 INFO @ Sat, 03 Apr 2021 08:49:07: 25000000 INFO @ Sat, 03 Apr 2021 08:49:07: 18000000 INFO @ Sat, 03 Apr 2021 08:49:12: 14000000 INFO @ Sat, 03 Apr 2021 08:49:14: 26000000 INFO @ Sat, 03 Apr 2021 08:49:15: 19000000 INFO @ Sat, 03 Apr 2021 08:49:20: 15000000 INFO @ Sat, 03 Apr 2021 08:49:20: 27000000 INFO @ Sat, 03 Apr 2021 08:49:23: 20000000 INFO @ Sat, 03 Apr 2021 08:49:27: 28000000 INFO @ Sat, 03 Apr 2021 08:49:29: 16000000 INFO @ Sat, 03 Apr 2021 08:49:30: 21000000 INFO @ Sat, 03 Apr 2021 08:49:34: 29000000 INFO @ Sat, 03 Apr 2021 08:49:37: 17000000 INFO @ Sat, 03 Apr 2021 08:49:38: 22000000 INFO @ Sat, 03 Apr 2021 08:49:41: 30000000 INFO @ Sat, 03 Apr 2021 08:49:45: 23000000 INFO @ Sat, 03 Apr 2021 08:49:46: 18000000 INFO @ Sat, 03 Apr 2021 08:49:48: 31000000 INFO @ Sat, 03 Apr 2021 08:49:52: 24000000 INFO @ Sat, 03 Apr 2021 08:49:54: 19000000 INFO @ Sat, 03 Apr 2021 08:49:55: 32000000 INFO @ Sat, 03 Apr 2021 08:49:56: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:49:56: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:49:56: #1 total tags in treatment: 12247076 INFO @ Sat, 03 Apr 2021 08:49:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:49:56: #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 08:49:56: #1 tags after filtering in treatment: 9577537 INFO @ Sat, 03 Apr 2021 08:49:56: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 08:49:56: #1 finished! INFO @ Sat, 03 Apr 2021 08:49:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:49:57: #2 number of paired peaks: 443 WARNING @ Sat, 03 Apr 2021 08:49:57: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sat, 03 Apr 2021 08:49:57: start model_add_line... INFO @ Sat, 03 Apr 2021 08:49:57: start X-correlation... INFO @ Sat, 03 Apr 2021 08:49:57: end of X-cor INFO @ Sat, 03 Apr 2021 08:49:57: #2 finished! INFO @ Sat, 03 Apr 2021 08:49:57: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 08:49:57: #2 alternative fragment length(s) may be 4,88 bps INFO @ Sat, 03 Apr 2021 08:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.05_model.r WARNING @ Sat, 03 Apr 2021 08:49:57: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:49:57: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Sat, 03 Apr 2021 08:49:57: #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 08:49:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:50:00: 25000000 INFO @ Sat, 03 Apr 2021 08:50:03: 20000000 INFO @ Sat, 03 Apr 2021 08:50:07: 26000000 INFO @ Sat, 03 Apr 2021 08:50:11: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:50:14: 27000000 INFO @ Sat, 03 Apr 2021 08:50:20: 22000000 INFO @ Sat, 03 Apr 2021 08:50:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:50:22: 28000000 INFO @ Sat, 03 Apr 2021 08:50:28: 23000000 INFO @ Sat, 03 Apr 2021 08:50:29: 29000000 INFO @ Sat, 03 Apr 2021 08:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.05_summits.bed INFO @ Sat, 03 Apr 2021 08:50:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7081 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:50:36: 24000000 INFO @ Sat, 03 Apr 2021 08:50:37: 30000000 INFO @ Sat, 03 Apr 2021 08:50:44: 31000000 INFO @ Sat, 03 Apr 2021 08:50:44: 25000000 INFO @ Sat, 03 Apr 2021 08:50:52: 32000000 INFO @ Sat, 03 Apr 2021 08:50:52: 26000000 INFO @ Sat, 03 Apr 2021 08:50:53: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:50:53: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:50:53: #1 total tags in treatment: 12247076 INFO @ Sat, 03 Apr 2021 08:50:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:50:53: #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 08:50:53: #1 tags after filtering in treatment: 9577537 INFO @ Sat, 03 Apr 2021 08:50:53: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 08:50:53: #1 finished! INFO @ Sat, 03 Apr 2021 08:50:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:50:54: #2 number of paired peaks: 443 WARNING @ Sat, 03 Apr 2021 08:50:54: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sat, 03 Apr 2021 08:50:54: start model_add_line... INFO @ Sat, 03 Apr 2021 08:50:54: start X-correlation... INFO @ Sat, 03 Apr 2021 08:50:54: end of X-cor INFO @ Sat, 03 Apr 2021 08:50:54: #2 finished! INFO @ Sat, 03 Apr 2021 08:50:54: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 08:50:54: #2 alternative fragment length(s) may be 4,88 bps INFO @ Sat, 03 Apr 2021 08:50:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.10_model.r WARNING @ Sat, 03 Apr 2021 08:50:54: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:50:54: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Sat, 03 Apr 2021 08:50:54: #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 08:50:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:50:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:51:00: 27000000 INFO @ Sat, 03 Apr 2021 08:51:08: 28000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:51:16: 29000000 INFO @ Sat, 03 Apr 2021 08:51:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:51:24: 30000000 INFO @ Sat, 03 Apr 2021 08:51:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:51:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:51:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.10_summits.bed INFO @ Sat, 03 Apr 2021 08:51:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2018 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:51:33: 31000000 INFO @ Sat, 03 Apr 2021 08:51:41: 32000000 INFO @ Sat, 03 Apr 2021 08:51:42: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:51:42: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:51:42: #1 total tags in treatment: 12247076 INFO @ Sat, 03 Apr 2021 08:51:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:51:42: #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 08:51:42: #1 tags after filtering in treatment: 9577537 INFO @ Sat, 03 Apr 2021 08:51:42: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 03 Apr 2021 08:51:42: #1 finished! INFO @ Sat, 03 Apr 2021 08:51:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:51:43: #2 number of paired peaks: 443 WARNING @ Sat, 03 Apr 2021 08:51:43: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Sat, 03 Apr 2021 08:51:43: start model_add_line... INFO @ Sat, 03 Apr 2021 08:51:43: start X-correlation... INFO @ Sat, 03 Apr 2021 08:51:43: end of X-cor INFO @ Sat, 03 Apr 2021 08:51:43: #2 finished! INFO @ Sat, 03 Apr 2021 08:51:43: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 08:51:43: #2 alternative fragment length(s) may be 4,88 bps INFO @ Sat, 03 Apr 2021 08:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.20_model.r WARNING @ Sat, 03 Apr 2021 08:51:43: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:51:43: #2 You may need to consider one of the other alternative d(s): 4,88 WARNING @ Sat, 03 Apr 2021 08:51:43: #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 08:51:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:52:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277032/SRX7277032.20_summits.bed INFO @ Sat, 03 Apr 2021 08:52:17: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (241 records, 4 fields): 1 millis CompletedMACS2peakCalling