Job ID = 12265552 SRX = SRX7277019 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26508379 spots for SRR10597284/SRR10597284.sra Written 26508379 spots for SRR10597284/SRR10597284.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265914 ("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: 00:49:12 26508379 reads; of these: 26508379 (100.00%) were paired; of these: 10268926 (38.74%) aligned concordantly 0 times 10953575 (41.32%) aligned concordantly exactly 1 time 5285878 (19.94%) aligned concordantly >1 times ---- 10268926 pairs aligned concordantly 0 times; of these: 2444994 (23.81%) aligned discordantly 1 time ---- 7823932 pairs aligned 0 times concordantly or discordantly; of these: 15647864 mates make up the pairs; of these: 12541633 (80.15%) aligned 0 times 707604 (4.52%) aligned exactly 1 time 2398627 (15.33%) aligned >1 times 76.34% overall alignment rate Time searching: 00:49:12 Overall time: 00:49:12 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] 3088971 / 18545871 = 0.1666 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 08:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.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 08:41:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:41:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:42:00: 1000000 INFO @ Sat, 03 Apr 2021 08:42:07: 2000000 INFO @ Sat, 03 Apr 2021 08:42:14: 3000000 INFO @ Sat, 03 Apr 2021 08:42:20: 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 08:42:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.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 08:42:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:42:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:42:27: 5000000 INFO @ Sat, 03 Apr 2021 08:42:30: 1000000 INFO @ Sat, 03 Apr 2021 08:42:33: 6000000 INFO @ Sat, 03 Apr 2021 08:42:36: 2000000 INFO @ Sat, 03 Apr 2021 08:42:40: 7000000 INFO @ Sat, 03 Apr 2021 08:42:44: 3000000 INFO @ Sat, 03 Apr 2021 08:42:46: 8000000 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 08:42:51: 4000000 INFO @ Sat, 03 Apr 2021 08:42:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.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 08:42:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:42:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:42:53: 9000000 INFO @ Sat, 03 Apr 2021 08:42:58: 5000000 INFO @ Sat, 03 Apr 2021 08:43:00: 10000000 INFO @ Sat, 03 Apr 2021 08:43:01: 1000000 INFO @ Sat, 03 Apr 2021 08:43:06: 6000000 INFO @ Sat, 03 Apr 2021 08:43:06: 11000000 INFO @ Sat, 03 Apr 2021 08:43:08: 2000000 INFO @ Sat, 03 Apr 2021 08:43:13: 12000000 INFO @ Sat, 03 Apr 2021 08:43:14: 7000000 INFO @ Sat, 03 Apr 2021 08:43:16: 3000000 INFO @ Sat, 03 Apr 2021 08:43:19: 13000000 INFO @ Sat, 03 Apr 2021 08:43:21: 8000000 INFO @ Sat, 03 Apr 2021 08:43:24: 4000000 INFO @ Sat, 03 Apr 2021 08:43:26: 14000000 INFO @ Sat, 03 Apr 2021 08:43:29: 9000000 INFO @ Sat, 03 Apr 2021 08:43:31: 5000000 INFO @ Sat, 03 Apr 2021 08:43:33: 15000000 INFO @ Sat, 03 Apr 2021 08:43:37: 10000000 INFO @ Sat, 03 Apr 2021 08:43:39: 6000000 INFO @ Sat, 03 Apr 2021 08:43:39: 16000000 INFO @ Sat, 03 Apr 2021 08:43:45: 11000000 INFO @ Sat, 03 Apr 2021 08:43:46: 17000000 INFO @ Sat, 03 Apr 2021 08:43:46: 7000000 INFO @ Sat, 03 Apr 2021 08:43:52: 18000000 INFO @ Sat, 03 Apr 2021 08:43:52: 12000000 INFO @ Sat, 03 Apr 2021 08:43:54: 8000000 INFO @ Sat, 03 Apr 2021 08:43:59: 19000000 INFO @ Sat, 03 Apr 2021 08:44:00: 13000000 INFO @ Sat, 03 Apr 2021 08:44:01: 9000000 INFO @ Sat, 03 Apr 2021 08:44:05: 20000000 INFO @ Sat, 03 Apr 2021 08:44:08: 14000000 INFO @ Sat, 03 Apr 2021 08:44:09: 10000000 INFO @ Sat, 03 Apr 2021 08:44:12: 21000000 INFO @ Sat, 03 Apr 2021 08:44:16: 15000000 INFO @ Sat, 03 Apr 2021 08:44:17: 11000000 INFO @ Sat, 03 Apr 2021 08:44:18: 22000000 INFO @ Sat, 03 Apr 2021 08:44:24: 16000000 INFO @ Sat, 03 Apr 2021 08:44:24: 12000000 INFO @ Sat, 03 Apr 2021 08:44:25: 23000000 INFO @ Sat, 03 Apr 2021 08:44:31: 24000000 INFO @ Sat, 03 Apr 2021 08:44:32: 17000000 INFO @ Sat, 03 Apr 2021 08:44:32: 13000000 INFO @ Sat, 03 Apr 2021 08:44:38: 25000000 INFO @ Sat, 03 Apr 2021 08:44:39: 18000000 INFO @ Sat, 03 Apr 2021 08:44:39: 14000000 INFO @ Sat, 03 Apr 2021 08:44:44: 26000000 INFO @ Sat, 03 Apr 2021 08:44:47: 19000000 INFO @ Sat, 03 Apr 2021 08:44:47: 15000000 INFO @ Sat, 03 Apr 2021 08:44:52: 27000000 INFO @ Sat, 03 Apr 2021 08:44:55: 16000000 INFO @ Sat, 03 Apr 2021 08:44:56: 20000000 INFO @ Sat, 03 Apr 2021 08:45:00: 28000000 INFO @ Sat, 03 Apr 2021 08:45:04: 21000000 INFO @ Sat, 03 Apr 2021 08:45:04: 17000000 INFO @ Sat, 03 Apr 2021 08:45:07: 29000000 INFO @ Sat, 03 Apr 2021 08:45:13: 18000000 INFO @ Sat, 03 Apr 2021 08:45:14: 22000000 INFO @ Sat, 03 Apr 2021 08:45:14: 30000000 INFO @ Sat, 03 Apr 2021 08:45:21: 31000000 INFO @ Sat, 03 Apr 2021 08:45:22: 19000000 INFO @ Sat, 03 Apr 2021 08:45:22: 23000000 INFO @ Sat, 03 Apr 2021 08:45:29: 32000000 INFO @ Sat, 03 Apr 2021 08:45:30: 20000000 INFO @ Sat, 03 Apr 2021 08:45:30: 24000000 INFO @ Sat, 03 Apr 2021 08:45:37: 33000000 INFO @ Sat, 03 Apr 2021 08:45:39: 21000000 INFO @ Sat, 03 Apr 2021 08:45:39: 25000000 INFO @ Sat, 03 Apr 2021 08:45:45: 34000000 INFO @ Sat, 03 Apr 2021 08:45:47: 26000000 INFO @ Sat, 03 Apr 2021 08:45:48: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:45:48: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:45:48: #1 total tags in treatment: 13271402 INFO @ Sat, 03 Apr 2021 08:45:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:45:48: #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 08:45:48: 22000000 INFO @ Sat, 03 Apr 2021 08:45:48: #1 tags after filtering in treatment: 10729233 INFO @ Sat, 03 Apr 2021 08:45:48: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:45:48: #1 finished! INFO @ Sat, 03 Apr 2021 08:45:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:45:49: #2 number of paired peaks: 152 WARNING @ Sat, 03 Apr 2021 08:45:49: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Sat, 03 Apr 2021 08:45:49: start model_add_line... INFO @ Sat, 03 Apr 2021 08:45:49: start X-correlation... INFO @ Sat, 03 Apr 2021 08:45:49: end of X-cor INFO @ Sat, 03 Apr 2021 08:45:49: #2 finished! INFO @ Sat, 03 Apr 2021 08:45:49: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 08:45:49: #2 alternative fragment length(s) may be 4,88,105,142,581 bps INFO @ Sat, 03 Apr 2021 08:45:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.05_model.r WARNING @ Sat, 03 Apr 2021 08:45:49: #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 08:45:49: #2 You may need to consider one of the other alternative d(s): 4,88,105,142,581 WARNING @ Sat, 03 Apr 2021 08:45:49: #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 08:45:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:45:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:45:55: 27000000 INFO @ Sat, 03 Apr 2021 08:45:56: 23000000 INFO @ Sat, 03 Apr 2021 08:46:04: 24000000 INFO @ Sat, 03 Apr 2021 08:46:06: 28000000 INFO @ Sat, 03 Apr 2021 08:46:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:46:12: 25000000 INFO @ Sat, 03 Apr 2021 08:46:15: 29000000 INFO @ Sat, 03 Apr 2021 08:46:21: 26000000 INFO @ Sat, 03 Apr 2021 08:46:23: 30000000 INFO @ Sat, 03 Apr 2021 08:46:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:46:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:46:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.05_summits.bed INFO @ Sat, 03 Apr 2021 08:46:25: Done! pass1 - making usageList (14 chroms): 11 millis pass2 - checking and writing primary data (4560 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:46:30: 27000000 INFO @ Sat, 03 Apr 2021 08:46:32: 31000000 INFO @ Sat, 03 Apr 2021 08:46:39: 28000000 INFO @ Sat, 03 Apr 2021 08:46:40: 32000000 INFO @ Sat, 03 Apr 2021 08:46:48: 33000000 INFO @ Sat, 03 Apr 2021 08:46:48: 29000000 INFO @ Sat, 03 Apr 2021 08:46:56: 30000000 INFO @ Sat, 03 Apr 2021 08:46:57: 34000000 INFO @ Sat, 03 Apr 2021 08:47:00: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:47:00: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:47:00: #1 total tags in treatment: 13271402 INFO @ Sat, 03 Apr 2021 08:47:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:47:00: #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 08:47:00: #1 tags after filtering in treatment: 10729233 INFO @ Sat, 03 Apr 2021 08:47:00: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:47:00: #1 finished! INFO @ Sat, 03 Apr 2021 08:47:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:47:01: #2 number of paired peaks: 152 WARNING @ Sat, 03 Apr 2021 08:47:01: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Sat, 03 Apr 2021 08:47:01: start model_add_line... INFO @ Sat, 03 Apr 2021 08:47:01: start X-correlation... INFO @ Sat, 03 Apr 2021 08:47:01: end of X-cor INFO @ Sat, 03 Apr 2021 08:47:01: #2 finished! INFO @ Sat, 03 Apr 2021 08:47:01: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 08:47:01: #2 alternative fragment length(s) may be 4,88,105,142,581 bps INFO @ Sat, 03 Apr 2021 08:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.10_model.r WARNING @ Sat, 03 Apr 2021 08:47:01: #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 08:47:01: #2 You may need to consider one of the other alternative d(s): 4,88,105,142,581 WARNING @ Sat, 03 Apr 2021 08:47:01: #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 08:47:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:47:03: 31000000 INFO @ Sat, 03 Apr 2021 08:47:11: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:47:20: 33000000 INFO @ Sat, 03 Apr 2021 08:47:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:47:28: 34000000 INFO @ Sat, 03 Apr 2021 08:47:30: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:47:30: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:47:30: #1 total tags in treatment: 13271402 INFO @ Sat, 03 Apr 2021 08:47:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:47:30: #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 08:47:30: #1 tags after filtering in treatment: 10729233 INFO @ Sat, 03 Apr 2021 08:47:30: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:47:30: #1 finished! INFO @ Sat, 03 Apr 2021 08:47:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:47:31: #2 number of paired peaks: 152 WARNING @ Sat, 03 Apr 2021 08:47:31: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Sat, 03 Apr 2021 08:47:31: start model_add_line... INFO @ Sat, 03 Apr 2021 08:47:31: start X-correlation... INFO @ Sat, 03 Apr 2021 08:47:31: end of X-cor INFO @ Sat, 03 Apr 2021 08:47:31: #2 finished! INFO @ Sat, 03 Apr 2021 08:47:31: #2 predicted fragment length is 88 bps INFO @ Sat, 03 Apr 2021 08:47:31: #2 alternative fragment length(s) may be 4,88,105,142,581 bps INFO @ Sat, 03 Apr 2021 08:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.20_model.r WARNING @ Sat, 03 Apr 2021 08:47:31: #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 08:47:31: #2 You may need to consider one of the other alternative d(s): 4,88,105,142,581 WARNING @ Sat, 03 Apr 2021 08:47:31: #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 08:47:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:47:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:47:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:47:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.10_summits.bed INFO @ Sat, 03 Apr 2021 08:47:36: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (873 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:47:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277019/SRX7277019.20_summits.bed INFO @ Sat, 03 Apr 2021 08:48:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。