Job ID = 12265260 SRX = SRX4664639 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22879823 spots for SRR7813066/SRR7813066.sra Written 22879823 spots for SRR7813066/SRR7813066.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265613 ("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: 00:58:28 22879823 reads; of these: 22879823 (100.00%) were paired; of these: 7913473 (34.59%) aligned concordantly 0 times 8249233 (36.05%) aligned concordantly exactly 1 time 6717117 (29.36%) aligned concordantly >1 times ---- 7913473 pairs aligned concordantly 0 times; of these: 2407352 (30.42%) aligned discordantly 1 time ---- 5506121 pairs aligned 0 times concordantly or discordantly; of these: 11012242 mates make up the pairs; of these: 7541043 (68.48%) aligned 0 times 906035 (8.23%) aligned exactly 1 time 2565164 (23.29%) aligned >1 times 83.52% overall alignment rate Time searching: 00:58:28 Overall time: 00:58:28 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] 2657239 / 17056089 = 0.1558 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 07:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.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 07:31:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:31:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:31:46: 1000000 INFO @ Sat, 03 Apr 2021 07:31:51: 2000000 INFO @ Sat, 03 Apr 2021 07:31:56: 3000000 INFO @ Sat, 03 Apr 2021 07:32:01: 4000000 INFO @ Sat, 03 Apr 2021 07:32:06: 5000000 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 07:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.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 07:32:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:32:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:32:11: 6000000 INFO @ Sat, 03 Apr 2021 07:32:16: 1000000 INFO @ Sat, 03 Apr 2021 07:32:16: 7000000 INFO @ Sat, 03 Apr 2021 07:32:22: 8000000 INFO @ Sat, 03 Apr 2021 07:32:22: 2000000 INFO @ Sat, 03 Apr 2021 07:32:27: 9000000 INFO @ Sat, 03 Apr 2021 07:32:28: 3000000 INFO @ Sat, 03 Apr 2021 07:32:32: 10000000 INFO @ Sat, 03 Apr 2021 07:32:33: 4000000 INFO @ Sat, 03 Apr 2021 07:32:37: 11000000 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 07:32:39: 5000000 INFO @ Sat, 03 Apr 2021 07:32:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.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 07:32:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:32:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:32:43: 12000000 INFO @ Sat, 03 Apr 2021 07:32:44: 6000000 INFO @ Sat, 03 Apr 2021 07:32:46: 1000000 INFO @ Sat, 03 Apr 2021 07:32:48: 13000000 INFO @ Sat, 03 Apr 2021 07:32:50: 7000000 INFO @ Sat, 03 Apr 2021 07:32:52: 2000000 INFO @ Sat, 03 Apr 2021 07:32:54: 14000000 INFO @ Sat, 03 Apr 2021 07:32:55: 8000000 INFO @ Sat, 03 Apr 2021 07:32:58: 3000000 INFO @ Sat, 03 Apr 2021 07:33:00: 15000000 INFO @ Sat, 03 Apr 2021 07:33:01: 9000000 INFO @ Sat, 03 Apr 2021 07:33:03: 4000000 INFO @ Sat, 03 Apr 2021 07:33:05: 16000000 INFO @ Sat, 03 Apr 2021 07:33:07: 10000000 INFO @ Sat, 03 Apr 2021 07:33:09: 5000000 INFO @ Sat, 03 Apr 2021 07:33:11: 17000000 INFO @ Sat, 03 Apr 2021 07:33:12: 11000000 INFO @ Sat, 03 Apr 2021 07:33:15: 6000000 INFO @ Sat, 03 Apr 2021 07:33:17: 18000000 INFO @ Sat, 03 Apr 2021 07:33:18: 12000000 INFO @ Sat, 03 Apr 2021 07:33:20: 7000000 INFO @ Sat, 03 Apr 2021 07:33:22: 19000000 INFO @ Sat, 03 Apr 2021 07:33:24: 13000000 INFO @ Sat, 03 Apr 2021 07:33:26: 8000000 INFO @ Sat, 03 Apr 2021 07:33:28: 20000000 INFO @ Sat, 03 Apr 2021 07:33:31: 14000000 INFO @ Sat, 03 Apr 2021 07:33:32: 9000000 INFO @ Sat, 03 Apr 2021 07:33:34: 21000000 INFO @ Sat, 03 Apr 2021 07:33:37: 15000000 INFO @ Sat, 03 Apr 2021 07:33:37: 10000000 INFO @ Sat, 03 Apr 2021 07:33:39: 22000000 INFO @ Sat, 03 Apr 2021 07:33:43: 16000000 INFO @ Sat, 03 Apr 2021 07:33:43: 11000000 INFO @ Sat, 03 Apr 2021 07:33:45: 23000000 INFO @ Sat, 03 Apr 2021 07:33:49: 17000000 INFO @ Sat, 03 Apr 2021 07:33:49: 12000000 INFO @ Sat, 03 Apr 2021 07:33:50: 24000000 INFO @ Sat, 03 Apr 2021 07:33:55: 18000000 INFO @ Sat, 03 Apr 2021 07:33:55: 13000000 INFO @ Sat, 03 Apr 2021 07:33:56: 25000000 INFO @ Sat, 03 Apr 2021 07:34:01: 19000000 INFO @ Sat, 03 Apr 2021 07:34:01: 14000000 INFO @ Sat, 03 Apr 2021 07:34:02: 26000000 INFO @ Sat, 03 Apr 2021 07:34:06: 20000000 INFO @ Sat, 03 Apr 2021 07:34:07: 15000000 INFO @ Sat, 03 Apr 2021 07:34:08: 27000000 INFO @ Sat, 03 Apr 2021 07:34:12: 21000000 INFO @ Sat, 03 Apr 2021 07:34:13: 16000000 INFO @ Sat, 03 Apr 2021 07:34:14: 28000000 INFO @ Sat, 03 Apr 2021 07:34:18: 22000000 INFO @ Sat, 03 Apr 2021 07:34:19: 17000000 INFO @ Sat, 03 Apr 2021 07:34:19: 29000000 INFO @ Sat, 03 Apr 2021 07:34:23: 23000000 INFO @ Sat, 03 Apr 2021 07:34:24: 18000000 INFO @ Sat, 03 Apr 2021 07:34:25: 30000000 INFO @ Sat, 03 Apr 2021 07:34:29: 24000000 INFO @ Sat, 03 Apr 2021 07:34:30: 19000000 INFO @ Sat, 03 Apr 2021 07:34:31: 31000000 INFO @ Sat, 03 Apr 2021 07:34:35: 25000000 INFO @ Sat, 03 Apr 2021 07:34:36: 20000000 INFO @ Sat, 03 Apr 2021 07:34:37: 32000000 INFO @ Sat, 03 Apr 2021 07:34:40: 26000000 INFO @ Sat, 03 Apr 2021 07:34:42: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:34:42: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:34:42: #1 total tags in treatment: 12478152 INFO @ Sat, 03 Apr 2021 07:34:42: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:34:42: #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 07:34:42: 21000000 INFO @ Sat, 03 Apr 2021 07:34:42: #1 tags after filtering in treatment: 10208573 INFO @ Sat, 03 Apr 2021 07:34:42: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:34:42: #1 finished! INFO @ Sat, 03 Apr 2021 07:34:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:34:43: #2 number of paired peaks: 599 WARNING @ Sat, 03 Apr 2021 07:34:43: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Sat, 03 Apr 2021 07:34:43: start model_add_line... INFO @ Sat, 03 Apr 2021 07:34:43: start X-correlation... INFO @ Sat, 03 Apr 2021 07:34:43: end of X-cor INFO @ Sat, 03 Apr 2021 07:34:43: #2 finished! INFO @ Sat, 03 Apr 2021 07:34:43: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 07:34:43: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sat, 03 Apr 2021 07:34:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.05_model.r WARNING @ Sat, 03 Apr 2021 07:34:43: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:34:43: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sat, 03 Apr 2021 07:34:43: #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 07:34:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:34:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:34:46: 27000000 INFO @ Sat, 03 Apr 2021 07:34:47: 22000000 INFO @ Sat, 03 Apr 2021 07:34:51: 28000000 INFO @ Sat, 03 Apr 2021 07:34:52: 23000000 INFO @ Sat, 03 Apr 2021 07:34:57: 29000000 INFO @ Sat, 03 Apr 2021 07:34:58: 24000000 INFO @ Sat, 03 Apr 2021 07:35:03: 30000000 INFO @ Sat, 03 Apr 2021 07:35:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:35:03: 25000000 INFO @ Sat, 03 Apr 2021 07:35:08: 31000000 INFO @ Sat, 03 Apr 2021 07:35:08: 26000000 INFO @ Sat, 03 Apr 2021 07:35:13: 32000000 INFO @ Sat, 03 Apr 2021 07:35:13: 27000000 INFO @ Sat, 03 Apr 2021 07:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.05_summits.bed INFO @ Sat, 03 Apr 2021 07:35:14: Done! pass1 - making usageList (15 chroms): 10 millis pass2 - checking and writing primary data (3671 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:35:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:35:18: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:35:18: #1 total tags in treatment: 12478152 INFO @ Sat, 03 Apr 2021 07:35:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:35:18: #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 07:35:18: #1 tags after filtering in treatment: 10208573 INFO @ Sat, 03 Apr 2021 07:35:18: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:35:18: #1 finished! INFO @ Sat, 03 Apr 2021 07:35:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:35:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:35:19: 28000000 INFO @ Sat, 03 Apr 2021 07:35:19: #2 number of paired peaks: 599 WARNING @ Sat, 03 Apr 2021 07:35:19: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Sat, 03 Apr 2021 07:35:19: start model_add_line... INFO @ Sat, 03 Apr 2021 07:35:19: start X-correlation... INFO @ Sat, 03 Apr 2021 07:35:19: end of X-cor INFO @ Sat, 03 Apr 2021 07:35:19: #2 finished! INFO @ Sat, 03 Apr 2021 07:35:19: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 07:35:19: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sat, 03 Apr 2021 07:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.10_model.r WARNING @ Sat, 03 Apr 2021 07:35:19: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:35:19: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sat, 03 Apr 2021 07:35:19: #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 07:35:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:35:24: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:35:29: 30000000 INFO @ Sat, 03 Apr 2021 07:35:34: 31000000 INFO @ Sat, 03 Apr 2021 07:35:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:35:39: 32000000 INFO @ Sat, 03 Apr 2021 07:35:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:35:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:35:43: #1 total tags in treatment: 12478152 INFO @ Sat, 03 Apr 2021 07:35:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:35:43: #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 07:35:43: #1 tags after filtering in treatment: 10208573 INFO @ Sat, 03 Apr 2021 07:35:43: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:35:43: #1 finished! INFO @ Sat, 03 Apr 2021 07:35:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:35:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:35:44: #2 number of paired peaks: 599 WARNING @ Sat, 03 Apr 2021 07:35:44: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Sat, 03 Apr 2021 07:35:44: start model_add_line... INFO @ Sat, 03 Apr 2021 07:35:44: start X-correlation... INFO @ Sat, 03 Apr 2021 07:35:44: end of X-cor INFO @ Sat, 03 Apr 2021 07:35:44: #2 finished! INFO @ Sat, 03 Apr 2021 07:35:44: #2 predicted fragment length is 87 bps INFO @ Sat, 03 Apr 2021 07:35:44: #2 alternative fragment length(s) may be 4,87 bps INFO @ Sat, 03 Apr 2021 07:35:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.20_model.r WARNING @ Sat, 03 Apr 2021 07:35:44: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:35:44: #2 You may need to consider one of the other alternative d(s): 4,87 WARNING @ Sat, 03 Apr 2021 07:35:44: #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 07:35:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:35:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:35:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:35:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.10_summits.bed INFO @ Sat, 03 Apr 2021 07:35:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1860 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:36:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664639/SRX4664639.20_summits.bed INFO @ Sat, 03 Apr 2021 07:36:14: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (665 records, 4 fields): 63 millis CompletedMACS2peakCalling BigWig に変換しました。