Job ID = 14170078 SRX = SRX8556368 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28468927 spots for SRR12024924/SRR12024924.sra Written 28468927 spots for SRR12024924/SRR12024924.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170878 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:46:10 28468927 reads; of these: 28468927 (100.00%) were paired; of these: 10406364 (36.55%) aligned concordantly 0 times 9006251 (31.64%) aligned concordantly exactly 1 time 9056312 (31.81%) aligned concordantly >1 times ---- 10406364 pairs aligned concordantly 0 times; of these: 2313589 (22.23%) aligned discordantly 1 time ---- 8092775 pairs aligned 0 times concordantly or discordantly; of these: 16185550 mates make up the pairs; of these: 11576821 (71.53%) aligned 0 times 486327 (3.00%) aligned exactly 1 time 4122402 (25.47%) aligned >1 times 79.67% overall alignment rate Time searching: 01:46:11 Overall time: 01:46:11 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] 5179644 / 20158908 = 0.2569 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.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, 11 Dec 2021 07:22:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:22:34: 1000000 INFO @ Sat, 11 Dec 2021 07:22:46: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:22:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.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, 11 Dec 2021 07:22:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:22:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:22:58: 3000000 INFO @ Sat, 11 Dec 2021 07:23:04: 1000000 INFO @ Sat, 11 Dec 2021 07:23:10: 4000000 INFO @ Sat, 11 Dec 2021 07:23:15: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:23:23: 5000000 INFO @ Sat, 11 Dec 2021 07:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.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, 11 Dec 2021 07:23:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:23:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:23:26: 3000000 INFO @ Sat, 11 Dec 2021 07:23:35: 1000000 INFO @ Sat, 11 Dec 2021 07:23:36: 6000000 INFO @ Sat, 11 Dec 2021 07:23:38: 4000000 INFO @ Sat, 11 Dec 2021 07:23:47: 2000000 INFO @ Sat, 11 Dec 2021 07:23:49: 7000000 INFO @ Sat, 11 Dec 2021 07:23:51: 5000000 INFO @ Sat, 11 Dec 2021 07:24:00: 3000000 INFO @ Sat, 11 Dec 2021 07:24:01: 8000000 INFO @ Sat, 11 Dec 2021 07:24:03: 6000000 INFO @ Sat, 11 Dec 2021 07:24:13: 4000000 INFO @ Sat, 11 Dec 2021 07:24:13: 9000000 INFO @ Sat, 11 Dec 2021 07:24:16: 7000000 INFO @ Sat, 11 Dec 2021 07:24:26: 5000000 INFO @ Sat, 11 Dec 2021 07:24:26: 10000000 INFO @ Sat, 11 Dec 2021 07:24:29: 8000000 INFO @ Sat, 11 Dec 2021 07:24:39: 11000000 INFO @ Sat, 11 Dec 2021 07:24:39: 6000000 INFO @ Sat, 11 Dec 2021 07:24:42: 9000000 INFO @ Sat, 11 Dec 2021 07:24:51: 7000000 INFO @ Sat, 11 Dec 2021 07:24:51: 12000000 INFO @ Sat, 11 Dec 2021 07:24:54: 10000000 INFO @ Sat, 11 Dec 2021 07:25:04: 13000000 INFO @ Sat, 11 Dec 2021 07:25:04: 8000000 INFO @ Sat, 11 Dec 2021 07:25:06: 11000000 INFO @ Sat, 11 Dec 2021 07:25:16: 9000000 INFO @ Sat, 11 Dec 2021 07:25:16: 14000000 INFO @ Sat, 11 Dec 2021 07:25:18: 12000000 INFO @ Sat, 11 Dec 2021 07:25:28: 10000000 INFO @ Sat, 11 Dec 2021 07:25:29: 15000000 INFO @ Sat, 11 Dec 2021 07:25:31: 13000000 INFO @ Sat, 11 Dec 2021 07:25:41: 11000000 INFO @ Sat, 11 Dec 2021 07:25:41: 16000000 INFO @ Sat, 11 Dec 2021 07:25:43: 14000000 INFO @ Sat, 11 Dec 2021 07:25:54: 12000000 INFO @ Sat, 11 Dec 2021 07:25:54: 17000000 INFO @ Sat, 11 Dec 2021 07:25:56: 15000000 INFO @ Sat, 11 Dec 2021 07:26:07: 13000000 INFO @ Sat, 11 Dec 2021 07:26:07: 18000000 INFO @ Sat, 11 Dec 2021 07:26:09: 16000000 INFO @ Sat, 11 Dec 2021 07:26:20: 14000000 INFO @ Sat, 11 Dec 2021 07:26:21: 19000000 INFO @ Sat, 11 Dec 2021 07:26:21: 17000000 INFO @ Sat, 11 Dec 2021 07:26:33: 15000000 INFO @ Sat, 11 Dec 2021 07:26:33: 20000000 INFO @ Sat, 11 Dec 2021 07:26:34: 18000000 INFO @ Sat, 11 Dec 2021 07:26:45: 21000000 INFO @ Sat, 11 Dec 2021 07:26:46: 19000000 INFO @ Sat, 11 Dec 2021 07:26:48: 16000000 INFO @ Sat, 11 Dec 2021 07:26:58: 20000000 INFO @ Sat, 11 Dec 2021 07:26:59: 22000000 INFO @ Sat, 11 Dec 2021 07:27:03: 17000000 INFO @ Sat, 11 Dec 2021 07:27:10: 21000000 INFO @ Sat, 11 Dec 2021 07:27:11: 23000000 INFO @ Sat, 11 Dec 2021 07:27:19: 18000000 INFO @ Sat, 11 Dec 2021 07:27:22: 22000000 INFO @ Sat, 11 Dec 2021 07:27:23: 24000000 INFO @ Sat, 11 Dec 2021 07:27:34: 19000000 INFO @ Sat, 11 Dec 2021 07:27:35: 23000000 INFO @ Sat, 11 Dec 2021 07:27:36: 25000000 INFO @ Sat, 11 Dec 2021 07:27:47: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:27:47: 26000000 INFO @ Sat, 11 Dec 2021 07:27:48: 20000000 INFO @ Sat, 11 Dec 2021 07:27:57: 25000000 INFO @ Sat, 11 Dec 2021 07:28:00: 27000000 INFO @ Sat, 11 Dec 2021 07:28:02: 21000000 INFO @ Sat, 11 Dec 2021 07:28:08: 26000000 INFO @ Sat, 11 Dec 2021 07:28:14: 28000000 INFO @ Sat, 11 Dec 2021 07:28:15: 22000000 INFO @ Sat, 11 Dec 2021 07:28:18: 27000000 INFO @ Sat, 11 Dec 2021 07:28:27: 29000000 INFO @ Sat, 11 Dec 2021 07:28:28: 23000000 INFO @ Sat, 11 Dec 2021 07:28:30: 28000000 INFO @ Sat, 11 Dec 2021 07:28:39: 30000000 INFO @ Sat, 11 Dec 2021 07:28:40: 24000000 INFO @ Sat, 11 Dec 2021 07:28:41: 29000000 INFO @ Sat, 11 Dec 2021 07:28:51: 31000000 INFO @ Sat, 11 Dec 2021 07:28:53: 30000000 INFO @ Sat, 11 Dec 2021 07:28:54: 25000000 INFO @ Sat, 11 Dec 2021 07:29:03: 32000000 INFO @ Sat, 11 Dec 2021 07:29:05: 31000000 INFO @ Sat, 11 Dec 2021 07:29:07: 26000000 INFO @ Sat, 11 Dec 2021 07:29:14: 33000000 INFO @ Sat, 11 Dec 2021 07:29:16: 32000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:29:21: 27000000 INFO @ Sat, 11 Dec 2021 07:29:26: 34000000 INFO @ Sat, 11 Dec 2021 07:29:27: 33000000 INFO @ Sat, 11 Dec 2021 07:29:36: 28000000 INFO @ Sat, 11 Dec 2021 07:29:37: 34000000 INFO @ Sat, 11 Dec 2021 07:29:38: 35000000 INFO @ Sat, 11 Dec 2021 07:29:38: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:29:38: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:29:38: #1 total tags in treatment: 13124499 INFO @ Sat, 11 Dec 2021 07:29:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:29:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:29:38: #1 tags after filtering in treatment: 10270445 INFO @ Sat, 11 Dec 2021 07:29:38: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 07:29:38: #1 finished! INFO @ Sat, 11 Dec 2021 07:29:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:29:39: #2 number of paired peaks: 145 WARNING @ Sat, 11 Dec 2021 07:29:39: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sat, 11 Dec 2021 07:29:39: start model_add_line... INFO @ Sat, 11 Dec 2021 07:29:39: start X-correlation... INFO @ Sat, 11 Dec 2021 07:29:39: end of X-cor INFO @ Sat, 11 Dec 2021 07:29:39: #2 finished! INFO @ Sat, 11 Dec 2021 07:29:39: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Dec 2021 07:29:39: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Dec 2021 07:29:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.05_model.r WARNING @ Sat, 11 Dec 2021 07:29:39: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:29:39: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 11 Dec 2021 07:29:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:29:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:29:48: 35000000 INFO @ Sat, 11 Dec 2021 07:29:48: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:29:48: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:29:48: #1 total tags in treatment: 13124499 INFO @ Sat, 11 Dec 2021 07:29:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:29:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:29:48: #1 tags after filtering in treatment: 10270445 INFO @ Sat, 11 Dec 2021 07:29:48: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 07:29:48: #1 finished! INFO @ Sat, 11 Dec 2021 07:29:48: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:29:49: #2 number of paired peaks: 145 WARNING @ Sat, 11 Dec 2021 07:29:49: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sat, 11 Dec 2021 07:29:49: start model_add_line... INFO @ Sat, 11 Dec 2021 07:29:49: start X-correlation... INFO @ Sat, 11 Dec 2021 07:29:49: end of X-cor INFO @ Sat, 11 Dec 2021 07:29:49: #2 finished! INFO @ Sat, 11 Dec 2021 07:29:49: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Dec 2021 07:29:49: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Dec 2021 07:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.10_model.r WARNING @ Sat, 11 Dec 2021 07:29:49: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:29:49: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 11 Dec 2021 07:29:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:29:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:29:52: 29000000 INFO @ Sat, 11 Dec 2021 07:30:08: 30000000 INFO @ Sat, 11 Dec 2021 07:30:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:30:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:30:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:30:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:30:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.05_summits.bed INFO @ Sat, 11 Dec 2021 07:30:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2436 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:30:24: 31000000 INFO @ Sat, 11 Dec 2021 07:30:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:30:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:30:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.10_summits.bed INFO @ Sat, 11 Dec 2021 07:30:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:30:40: 32000000 INFO @ Sat, 11 Dec 2021 07:30:56: 33000000 INFO @ Sat, 11 Dec 2021 07:31:13: 34000000 INFO @ Sat, 11 Dec 2021 07:31:29: 35000000 INFO @ Sat, 11 Dec 2021 07:31:29: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 07:31:29: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 07:31:29: #1 total tags in treatment: 13124499 INFO @ Sat, 11 Dec 2021 07:31:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:31:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:31:30: #1 tags after filtering in treatment: 10270445 INFO @ Sat, 11 Dec 2021 07:31:30: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 07:31:30: #1 finished! INFO @ Sat, 11 Dec 2021 07:31:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:31:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:31:31: #2 number of paired peaks: 145 WARNING @ Sat, 11 Dec 2021 07:31:31: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Sat, 11 Dec 2021 07:31:31: start model_add_line... INFO @ Sat, 11 Dec 2021 07:31:31: start X-correlation... INFO @ Sat, 11 Dec 2021 07:31:31: end of X-cor INFO @ Sat, 11 Dec 2021 07:31:31: #2 finished! INFO @ Sat, 11 Dec 2021 07:31:31: #2 predicted fragment length is 176 bps INFO @ Sat, 11 Dec 2021 07:31:31: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 11 Dec 2021 07:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.20_model.r WARNING @ Sat, 11 Dec 2021 07:31:31: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:31:31: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Sat, 11 Dec 2021 07:31:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:31:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:32:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556368/SRX8556368.20_summits.bed INFO @ Sat, 11 Dec 2021 07:32:14: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (411 records, 4 fields): 2 millis CompletedMACS2peakCalling