Job ID = 12265177 SRX = SRX3141077 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 51231154 spots for SRR5985083/SRR5985083.sra Written 51231154 spots for SRR5985083/SRR5985083.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265851 ("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: 01:38:54 51231154 reads; of these: 51231154 (100.00%) were paired; of these: 30738114 (60.00%) aligned concordantly 0 times 11249551 (21.96%) aligned concordantly exactly 1 time 9243489 (18.04%) aligned concordantly >1 times ---- 30738114 pairs aligned concordantly 0 times; of these: 4462214 (14.52%) aligned discordantly 1 time ---- 26275900 pairs aligned 0 times concordantly or discordantly; of these: 52551800 mates make up the pairs; of these: 44245247 (84.19%) aligned 0 times 1597565 (3.04%) aligned exactly 1 time 6708988 (12.77%) aligned >1 times 56.82% overall alignment rate Time searching: 01:38:54 Overall time: 01:38:54 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 24 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] 9133091 / 24544065 = 0.3721 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 08:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.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 08:45:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:45:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:45:23: 1000000 INFO @ Sat, 03 Apr 2021 08:45:32: 2000000 INFO @ Sat, 03 Apr 2021 08:45:40: 3000000 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 08:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.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 08:45:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:45:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:45:48: 4000000 INFO @ Sat, 03 Apr 2021 08:45:54: 1000000 INFO @ Sat, 03 Apr 2021 08:45:57: 5000000 INFO @ Sat, 03 Apr 2021 08:46:02: 2000000 INFO @ Sat, 03 Apr 2021 08:46:05: 6000000 INFO @ Sat, 03 Apr 2021 08:46:11: 3000000 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 08:46:14: 7000000 INFO @ Sat, 03 Apr 2021 08:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.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 08:46:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:46:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:46:19: 4000000 INFO @ Sat, 03 Apr 2021 08:46:22: 8000000 INFO @ Sat, 03 Apr 2021 08:46:23: 1000000 INFO @ Sat, 03 Apr 2021 08:46:27: 5000000 INFO @ Sat, 03 Apr 2021 08:46:31: 9000000 INFO @ Sat, 03 Apr 2021 08:46:31: 2000000 INFO @ Sat, 03 Apr 2021 08:46:35: 6000000 INFO @ Sat, 03 Apr 2021 08:46:39: 3000000 INFO @ Sat, 03 Apr 2021 08:46:39: 10000000 INFO @ Sat, 03 Apr 2021 08:46:43: 7000000 INFO @ Sat, 03 Apr 2021 08:46:46: 4000000 INFO @ Sat, 03 Apr 2021 08:46:47: 11000000 INFO @ Sat, 03 Apr 2021 08:46:50: 8000000 INFO @ Sat, 03 Apr 2021 08:46:54: 5000000 INFO @ Sat, 03 Apr 2021 08:46:56: 12000000 INFO @ Sat, 03 Apr 2021 08:46:58: 9000000 INFO @ Sat, 03 Apr 2021 08:47:01: 6000000 INFO @ Sat, 03 Apr 2021 08:47:04: 13000000 INFO @ Sat, 03 Apr 2021 08:47:05: 10000000 INFO @ Sat, 03 Apr 2021 08:47:08: 7000000 INFO @ Sat, 03 Apr 2021 08:47:11: 14000000 INFO @ Sat, 03 Apr 2021 08:47:13: 11000000 INFO @ Sat, 03 Apr 2021 08:47:16: 8000000 INFO @ Sat, 03 Apr 2021 08:47:19: 15000000 INFO @ Sat, 03 Apr 2021 08:47:21: 12000000 INFO @ Sat, 03 Apr 2021 08:47:23: 9000000 INFO @ Sat, 03 Apr 2021 08:47:26: 16000000 INFO @ Sat, 03 Apr 2021 08:47:28: 13000000 INFO @ Sat, 03 Apr 2021 08:47:31: 10000000 INFO @ Sat, 03 Apr 2021 08:47:34: 17000000 INFO @ Sat, 03 Apr 2021 08:47:36: 14000000 INFO @ Sat, 03 Apr 2021 08:47:38: 11000000 INFO @ Sat, 03 Apr 2021 08:47:41: 18000000 INFO @ Sat, 03 Apr 2021 08:47:43: 15000000 INFO @ Sat, 03 Apr 2021 08:47:45: 12000000 INFO @ Sat, 03 Apr 2021 08:47:48: 19000000 INFO @ Sat, 03 Apr 2021 08:47:50: 16000000 INFO @ Sat, 03 Apr 2021 08:47:52: 13000000 INFO @ Sat, 03 Apr 2021 08:47:56: 20000000 INFO @ Sat, 03 Apr 2021 08:47:57: 17000000 INFO @ Sat, 03 Apr 2021 08:48:00: 14000000 INFO @ Sat, 03 Apr 2021 08:48:03: 21000000 INFO @ Sat, 03 Apr 2021 08:48:05: 18000000 INFO @ Sat, 03 Apr 2021 08:48:07: 15000000 INFO @ Sat, 03 Apr 2021 08:48:11: 22000000 INFO @ Sat, 03 Apr 2021 08:48:12: 19000000 INFO @ Sat, 03 Apr 2021 08:48:14: 16000000 INFO @ Sat, 03 Apr 2021 08:48:18: 23000000 INFO @ Sat, 03 Apr 2021 08:48:19: 20000000 INFO @ Sat, 03 Apr 2021 08:48:22: 17000000 INFO @ Sat, 03 Apr 2021 08:48:25: 24000000 INFO @ Sat, 03 Apr 2021 08:48:26: 21000000 INFO @ Sat, 03 Apr 2021 08:48:29: 18000000 INFO @ Sat, 03 Apr 2021 08:48:33: 25000000 INFO @ Sat, 03 Apr 2021 08:48:34: 22000000 INFO @ Sat, 03 Apr 2021 08:48:36: 19000000 INFO @ Sat, 03 Apr 2021 08:48:40: 26000000 INFO @ Sat, 03 Apr 2021 08:48:41: 23000000 INFO @ Sat, 03 Apr 2021 08:48:43: 20000000 INFO @ Sat, 03 Apr 2021 08:48:46: 27000000 INFO @ Sat, 03 Apr 2021 08:48:48: 24000000 INFO @ Sat, 03 Apr 2021 08:48:51: 21000000 INFO @ Sat, 03 Apr 2021 08:48:53: 28000000 INFO @ Sat, 03 Apr 2021 08:48:55: 25000000 INFO @ Sat, 03 Apr 2021 08:48:58: 22000000 INFO @ Sat, 03 Apr 2021 08:49:01: 29000000 INFO @ Sat, 03 Apr 2021 08:49:02: 26000000 INFO @ Sat, 03 Apr 2021 08:49:05: 23000000 INFO @ Sat, 03 Apr 2021 08:49:08: 30000000 INFO @ Sat, 03 Apr 2021 08:49:09: 27000000 INFO @ Sat, 03 Apr 2021 08:49:12: 24000000 INFO @ Sat, 03 Apr 2021 08:49:15: 28000000 INFO @ Sat, 03 Apr 2021 08:49:15: 31000000 INFO @ Sat, 03 Apr 2021 08:49:20: 25000000 INFO @ Sat, 03 Apr 2021 08:49:23: 29000000 INFO @ Sat, 03 Apr 2021 08:49:23: 32000000 INFO @ Sat, 03 Apr 2021 08:49:27: 26000000 INFO @ Sat, 03 Apr 2021 08:49:30: 30000000 INFO @ Sat, 03 Apr 2021 08:49:31: 33000000 INFO @ Sat, 03 Apr 2021 08:49:34: 27000000 INFO @ Sat, 03 Apr 2021 08:49:38: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:49:39: 34000000 INFO @ Sat, 03 Apr 2021 08:49:42: 28000000 INFO @ Sat, 03 Apr 2021 08:49:46: 32000000 INFO @ Sat, 03 Apr 2021 08:49:47: 35000000 INFO @ Sat, 03 Apr 2021 08:49:50: 29000000 INFO @ Sat, 03 Apr 2021 08:49:54: 33000000 INFO @ Sat, 03 Apr 2021 08:49:55: 36000000 INFO @ Sat, 03 Apr 2021 08:49:57: 30000000 INFO @ Sat, 03 Apr 2021 08:50:02: 34000000 INFO @ Sat, 03 Apr 2021 08:50:03: 37000000 INFO @ Sat, 03 Apr 2021 08:50:05: 31000000 INFO @ Sat, 03 Apr 2021 08:50:11: 35000000 INFO @ Sat, 03 Apr 2021 08:50:12: 38000000 INFO @ Sat, 03 Apr 2021 08:50:13: 32000000 INFO @ Sat, 03 Apr 2021 08:50:19: 36000000 INFO @ Sat, 03 Apr 2021 08:50:20: 39000000 INFO @ Sat, 03 Apr 2021 08:50:21: 33000000 INFO @ Sat, 03 Apr 2021 08:50:28: 37000000 INFO @ Sat, 03 Apr 2021 08:50:28: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 08:50:28: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 08:50:28: #1 total tags in treatment: 12988960 INFO @ Sat, 03 Apr 2021 08:50:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:50:28: #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 08:50:29: #1 tags after filtering in treatment: 9834478 INFO @ Sat, 03 Apr 2021 08:50:29: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 08:50:29: #1 finished! INFO @ Sat, 03 Apr 2021 08:50:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:50:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:50:29: #2 number of paired peaks: 1511 INFO @ Sat, 03 Apr 2021 08:50:29: start model_add_line... INFO @ Sat, 03 Apr 2021 08:50:29: 34000000 INFO @ Sat, 03 Apr 2021 08:50:29: start X-correlation... INFO @ Sat, 03 Apr 2021 08:50:29: end of X-cor INFO @ Sat, 03 Apr 2021 08:50:29: #2 finished! INFO @ Sat, 03 Apr 2021 08:50:29: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 08:50:29: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 08:50:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.05_model.r WARNING @ Sat, 03 Apr 2021 08:50:29: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:50:29: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 08:50:29: #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 08:50:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:50:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:50:36: 38000000 INFO @ Sat, 03 Apr 2021 08:50:37: 35000000 INFO @ Sat, 03 Apr 2021 08:50:44: 39000000 INFO @ Sat, 03 Apr 2021 08:50:45: 36000000 INFO @ Sat, 03 Apr 2021 08:50:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:50:52: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 08:50:52: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 08:50:52: #1 total tags in treatment: 12988960 INFO @ Sat, 03 Apr 2021 08:50:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:50:52: #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 08:50:53: #1 tags after filtering in treatment: 9834478 INFO @ Sat, 03 Apr 2021 08:50:53: #1 Redundant rate of treatment: 0.24 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 08:50:53: #2 number of paired peaks: 1511 INFO @ Sat, 03 Apr 2021 08:50:53: start model_add_line... INFO @ Sat, 03 Apr 2021 08:50:53: start X-correlation... INFO @ Sat, 03 Apr 2021 08:50:53: end of X-cor INFO @ Sat, 03 Apr 2021 08:50:53: #2 finished! INFO @ Sat, 03 Apr 2021 08:50:53: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 08:50:53: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 08:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.10_model.r WARNING @ Sat, 03 Apr 2021 08:50:53: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:50:53: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 08:50:53: #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 08:50:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:50:54: 37000000 INFO @ Sat, 03 Apr 2021 08:51:01: 38000000 INFO @ Sat, 03 Apr 2021 08:51:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:51:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:51:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.05_summits.bed INFO @ Sat, 03 Apr 2021 08:51:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6140 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:51:09: 39000000 INFO @ Sat, 03 Apr 2021 08:51:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:51:16: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 08:51:16: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 08:51:16: #1 total tags in treatment: 12988960 INFO @ Sat, 03 Apr 2021 08:51:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:51:16: #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 08:51:16: #1 tags after filtering in treatment: 9834478 INFO @ Sat, 03 Apr 2021 08:51:16: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 03 Apr 2021 08:51:16: #1 finished! INFO @ Sat, 03 Apr 2021 08:51:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:51:17: #2 number of paired peaks: 1511 INFO @ Sat, 03 Apr 2021 08:51:17: start model_add_line... INFO @ Sat, 03 Apr 2021 08:51:17: start X-correlation... INFO @ Sat, 03 Apr 2021 08:51:17: end of X-cor INFO @ Sat, 03 Apr 2021 08:51:17: #2 finished! INFO @ Sat, 03 Apr 2021 08:51:17: #2 predicted fragment length is 102 bps INFO @ Sat, 03 Apr 2021 08:51:17: #2 alternative fragment length(s) may be 102 bps INFO @ Sat, 03 Apr 2021 08:51:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.20_model.r WARNING @ Sat, 03 Apr 2021 08:51:17: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:51:17: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sat, 03 Apr 2021 08:51:17: #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 08:51:17: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:51:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.10_summits.bed INFO @ Sat, 03 Apr 2021 08:51:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3667 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:51:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:51:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:51:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:51:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3141077/SRX3141077.20_summits.bed INFO @ Sat, 03 Apr 2021 08:51:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1882 records, 4 fields): 5 millis CompletedMACS2peakCalling