Job ID = 14168796 SRX = ERX3978773 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29790889 spots for ERR3975792/ERR3975792.sra Written 29790889 spots for ERR3975792/ERR3975792.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169901 ("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: 00:53:24 29790889 reads; of these: 29790889 (100.00%) were paired; of these: 11922435 (40.02%) aligned concordantly 0 times 12040525 (40.42%) aligned concordantly exactly 1 time 5827929 (19.56%) aligned concordantly >1 times ---- 11922435 pairs aligned concordantly 0 times; of these: 3364834 (28.22%) aligned discordantly 1 time ---- 8557601 pairs aligned 0 times concordantly or discordantly; of these: 17115202 mates make up the pairs; of these: 12108178 (70.75%) aligned 0 times 711562 (4.16%) aligned exactly 1 time 4295462 (25.10%) aligned >1 times 79.68% overall alignment rate Time searching: 00:53:25 Overall time: 00:53:25 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 32 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] 5161162 / 21096534 = 0.2446 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 @ Fri, 10 Dec 2021 21:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.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 @ Fri, 10 Dec 2021 21:33:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:33:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:33:30: 1000000 INFO @ Fri, 10 Dec 2021 21:33:37: 2000000 INFO @ Fri, 10 Dec 2021 21:33:45: 3000000 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 @ Fri, 10 Dec 2021 21:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.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 @ Fri, 10 Dec 2021 21:33:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:33:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:33:52: 4000000 INFO @ Fri, 10 Dec 2021 21:33:58: 1000000 INFO @ Fri, 10 Dec 2021 21:34:00: 5000000 INFO @ Fri, 10 Dec 2021 21:34:05: 2000000 INFO @ Fri, 10 Dec 2021 21:34:08: 6000000 INFO @ Fri, 10 Dec 2021 21:34:11: 3000000 INFO @ Fri, 10 Dec 2021 21:34:17: 7000000 INFO @ Fri, 10 Dec 2021 21:34:18: 4000000 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 @ Fri, 10 Dec 2021 21:34:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.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 @ Fri, 10 Dec 2021 21:34:22: #1 read tag files... INFO @ Fri, 10 Dec 2021 21:34:22: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 21:34:25: 5000000 INFO @ Fri, 10 Dec 2021 21:34:25: 8000000 INFO @ Fri, 10 Dec 2021 21:34:30: 1000000 INFO @ Fri, 10 Dec 2021 21:34:31: 6000000 INFO @ Fri, 10 Dec 2021 21:34:33: 9000000 INFO @ Fri, 10 Dec 2021 21:34:38: 7000000 INFO @ Fri, 10 Dec 2021 21:34:38: 2000000 INFO @ Fri, 10 Dec 2021 21:34:41: 10000000 INFO @ Fri, 10 Dec 2021 21:34:44: 8000000 INFO @ Fri, 10 Dec 2021 21:34:46: 3000000 INFO @ Fri, 10 Dec 2021 21:34:49: 11000000 INFO @ Fri, 10 Dec 2021 21:34:51: 9000000 INFO @ Fri, 10 Dec 2021 21:34:54: 4000000 INFO @ Fri, 10 Dec 2021 21:34:58: 12000000 INFO @ Fri, 10 Dec 2021 21:34:58: 10000000 INFO @ Fri, 10 Dec 2021 21:35:02: 5000000 INFO @ Fri, 10 Dec 2021 21:35:05: 11000000 INFO @ Fri, 10 Dec 2021 21:35:06: 13000000 INFO @ Fri, 10 Dec 2021 21:35:09: 6000000 INFO @ Fri, 10 Dec 2021 21:35:11: 12000000 INFO @ Fri, 10 Dec 2021 21:35:14: 14000000 INFO @ Fri, 10 Dec 2021 21:35:17: 7000000 INFO @ Fri, 10 Dec 2021 21:35:18: 13000000 INFO @ Fri, 10 Dec 2021 21:35:22: 15000000 INFO @ Fri, 10 Dec 2021 21:35:25: 14000000 INFO @ Fri, 10 Dec 2021 21:35:25: 8000000 INFO @ Fri, 10 Dec 2021 21:35:31: 16000000 INFO @ Fri, 10 Dec 2021 21:35:31: 15000000 INFO @ Fri, 10 Dec 2021 21:35:33: 9000000 INFO @ Fri, 10 Dec 2021 21:35:38: 16000000 INFO @ Fri, 10 Dec 2021 21:35:38: 17000000 INFO @ Fri, 10 Dec 2021 21:35:41: 10000000 INFO @ Fri, 10 Dec 2021 21:35:45: 17000000 INFO @ Fri, 10 Dec 2021 21:35:46: 18000000 INFO @ Fri, 10 Dec 2021 21:35:49: 11000000 INFO @ Fri, 10 Dec 2021 21:35:51: 18000000 INFO @ Fri, 10 Dec 2021 21:35:54: 19000000 INFO @ Fri, 10 Dec 2021 21:35:57: 12000000 INFO @ Fri, 10 Dec 2021 21:35:58: 19000000 INFO @ Fri, 10 Dec 2021 21:36:02: 20000000 INFO @ Fri, 10 Dec 2021 21:36:05: 20000000 INFO @ Fri, 10 Dec 2021 21:36:05: 13000000 INFO @ Fri, 10 Dec 2021 21:36:10: 21000000 INFO @ Fri, 10 Dec 2021 21:36:11: 21000000 INFO @ Fri, 10 Dec 2021 21:36:13: 14000000 INFO @ Fri, 10 Dec 2021 21:36:18: 22000000 INFO @ Fri, 10 Dec 2021 21:36:19: 22000000 INFO @ Fri, 10 Dec 2021 21:36:21: 15000000 INFO @ Fri, 10 Dec 2021 21:36:26: 23000000 INFO @ Fri, 10 Dec 2021 21:36:27: 23000000 INFO @ Fri, 10 Dec 2021 21:36:29: 16000000 INFO @ Fri, 10 Dec 2021 21:36:35: 24000000 INFO @ Fri, 10 Dec 2021 21:36:35: 24000000 INFO @ Fri, 10 Dec 2021 21:36:37: 17000000 INFO @ Fri, 10 Dec 2021 21:36:43: 25000000 INFO @ Fri, 10 Dec 2021 21:36:44: 25000000 INFO @ Fri, 10 Dec 2021 21:36:45: 18000000 INFO @ Fri, 10 Dec 2021 21:36:51: 26000000 INFO @ Fri, 10 Dec 2021 21:36:52: 26000000 INFO @ Fri, 10 Dec 2021 21:36:53: 19000000 INFO @ Fri, 10 Dec 2021 21:36:59: 27000000 INFO @ Fri, 10 Dec 2021 21:37:00: 27000000 INFO @ Fri, 10 Dec 2021 21:37:00: 20000000 INFO @ Fri, 10 Dec 2021 21:37:07: 28000000 INFO @ Fri, 10 Dec 2021 21:37:08: 28000000 INFO @ Fri, 10 Dec 2021 21:37:08: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 21:37:15: 29000000 INFO @ Fri, 10 Dec 2021 21:37:15: 29000000 INFO @ Fri, 10 Dec 2021 21:37:16: 22000000 INFO @ Fri, 10 Dec 2021 21:37:22: 30000000 INFO @ Fri, 10 Dec 2021 21:37:23: 30000000 INFO @ Fri, 10 Dec 2021 21:37:24: 23000000 INFO @ Fri, 10 Dec 2021 21:37:31: 31000000 INFO @ Fri, 10 Dec 2021 21:37:31: 31000000 INFO @ Fri, 10 Dec 2021 21:37:33: 24000000 INFO @ Fri, 10 Dec 2021 21:37:39: 32000000 INFO @ Fri, 10 Dec 2021 21:37:39: 32000000 INFO @ Fri, 10 Dec 2021 21:37:41: 25000000 INFO @ Fri, 10 Dec 2021 21:37:47: 33000000 INFO @ Fri, 10 Dec 2021 21:37:48: 33000000 INFO @ Fri, 10 Dec 2021 21:37:48: 26000000 INFO @ Fri, 10 Dec 2021 21:37:55: 34000000 INFO @ Fri, 10 Dec 2021 21:37:55: 34000000 INFO @ Fri, 10 Dec 2021 21:37:56: 27000000 INFO @ Fri, 10 Dec 2021 21:38:03: 35000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 21:38:04: 28000000 INFO @ Fri, 10 Dec 2021 21:38:04: 35000000 INFO @ Fri, 10 Dec 2021 21:38:11: 29000000 INFO @ Fri, 10 Dec 2021 21:38:12: 36000000 INFO @ Fri, 10 Dec 2021 21:38:12: 36000000 INFO @ Fri, 10 Dec 2021 21:38:19: 30000000 INFO @ Fri, 10 Dec 2021 21:38:20: 37000000 INFO @ Fri, 10 Dec 2021 21:38:21: 37000000 INFO @ Fri, 10 Dec 2021 21:38:21: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:38:21: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:38:21: #1 total tags in treatment: 12992933 INFO @ Fri, 10 Dec 2021 21:38:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:38:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:38:22: #1 tags after filtering in treatment: 9330351 INFO @ Fri, 10 Dec 2021 21:38:22: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 21:38:22: #1 finished! INFO @ Fri, 10 Dec 2021 21:38:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:38:22: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:38:22: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:38:22: #1 total tags in treatment: 12992933 INFO @ Fri, 10 Dec 2021 21:38:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:38:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:38:22: #1 tags after filtering in treatment: 9330351 INFO @ Fri, 10 Dec 2021 21:38:22: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 21:38:22: #1 finished! INFO @ Fri, 10 Dec 2021 21:38:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:38:22: #2 number of paired peaks: 2946 INFO @ Fri, 10 Dec 2021 21:38:22: start model_add_line... INFO @ Fri, 10 Dec 2021 21:38:22: start X-correlation... INFO @ Fri, 10 Dec 2021 21:38:23: end of X-cor INFO @ Fri, 10 Dec 2021 21:38:23: #2 finished! INFO @ Fri, 10 Dec 2021 21:38:23: #2 predicted fragment length is 188 bps INFO @ Fri, 10 Dec 2021 21:38:23: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 10 Dec 2021 21:38:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.05_model.r WARNING @ Fri, 10 Dec 2021 21:38:23: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:38:23: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 10 Dec 2021 21:38:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:38:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:38:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:38:23: #2 number of paired peaks: 2946 INFO @ Fri, 10 Dec 2021 21:38:23: start model_add_line... INFO @ Fri, 10 Dec 2021 21:38:23: start X-correlation... INFO @ Fri, 10 Dec 2021 21:38:23: end of X-cor INFO @ Fri, 10 Dec 2021 21:38:23: #2 finished! INFO @ Fri, 10 Dec 2021 21:38:23: #2 predicted fragment length is 188 bps INFO @ Fri, 10 Dec 2021 21:38:23: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 10 Dec 2021 21:38:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.10_model.r WARNING @ Fri, 10 Dec 2021 21:38:23: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:38:23: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 10 Dec 2021 21:38:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:38:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:38:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:38:27: 31000000 INFO @ Fri, 10 Dec 2021 21:38:34: 32000000 INFO @ Fri, 10 Dec 2021 21:38:42: 33000000 INFO @ Fri, 10 Dec 2021 21:38:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:38:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:38:50: 34000000 INFO @ Fri, 10 Dec 2021 21:38:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.05_peaks.xls INFO @ Fri, 10 Dec 2021 21:38:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:38:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.05_summits.bed INFO @ Fri, 10 Dec 2021 21:38:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (13152 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:38:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.10_peaks.xls INFO @ Fri, 10 Dec 2021 21:38:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:38:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.10_summits.bed INFO @ Fri, 10 Dec 2021 21:38:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8284 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 21:38:57: 35000000 INFO @ Fri, 10 Dec 2021 21:39:05: 36000000 INFO @ Fri, 10 Dec 2021 21:39:13: 37000000 INFO @ Fri, 10 Dec 2021 21:39:14: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 21:39:14: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 21:39:14: #1 total tags in treatment: 12992933 INFO @ Fri, 10 Dec 2021 21:39:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 21:39:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 21:39:14: #1 tags after filtering in treatment: 9330351 INFO @ Fri, 10 Dec 2021 21:39:14: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 21:39:14: #1 finished! INFO @ Fri, 10 Dec 2021 21:39:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 21:39:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 21:39:15: #2 number of paired peaks: 2946 INFO @ Fri, 10 Dec 2021 21:39:15: start model_add_line... INFO @ Fri, 10 Dec 2021 21:39:15: start X-correlation... INFO @ Fri, 10 Dec 2021 21:39:15: end of X-cor INFO @ Fri, 10 Dec 2021 21:39:15: #2 finished! INFO @ Fri, 10 Dec 2021 21:39:15: #2 predicted fragment length is 188 bps INFO @ Fri, 10 Dec 2021 21:39:15: #2 alternative fragment length(s) may be 188 bps INFO @ Fri, 10 Dec 2021 21:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.20_model.r WARNING @ Fri, 10 Dec 2021 21:39:15: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 21:39:15: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Fri, 10 Dec 2021 21:39:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 21:39:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 21:39:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 21:39:36: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 21:39:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.20_peaks.xls INFO @ Fri, 10 Dec 2021 21:39:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 21:39:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978773/ERX3978773.20_summits.bed INFO @ Fri, 10 Dec 2021 21:39:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3498 records, 4 fields): 4 millis CompletedMACS2peakCalling