Job ID = 14167060 SRX = SRX10412049 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36023394 spots for SRR14035711/SRR14035711.sra Written 36023394 spots for SRR14035711/SRR14035711.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167657 ("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: 01:12:45 36023394 reads; of these: 36023394 (100.00%) were paired; of these: 17921703 (49.75%) aligned concordantly 0 times 16001314 (44.42%) aligned concordantly exactly 1 time 2100377 (5.83%) aligned concordantly >1 times ---- 17921703 pairs aligned concordantly 0 times; of these: 5467007 (30.50%) aligned discordantly 1 time ---- 12454696 pairs aligned 0 times concordantly or discordantly; of these: 24909392 mates make up the pairs; of these: 22261390 (89.37%) aligned 0 times 1347363 (5.41%) aligned exactly 1 time 1300639 (5.22%) aligned >1 times 69.10% overall alignment rate Time searching: 01:12:45 Overall time: 01:12:45 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 40 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] 4829426 / 23472265 = 0.2058 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 11:05:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.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 11:05:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:05:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:05:48: 1000000 INFO @ Fri, 10 Dec 2021 11:05:56: 2000000 INFO @ Fri, 10 Dec 2021 11:06:04: 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 11:06:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.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 11:06:10: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:06:10: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:06:13: 4000000 INFO @ Fri, 10 Dec 2021 11:06:17: 1000000 INFO @ Fri, 10 Dec 2021 11:06:21: 5000000 INFO @ Fri, 10 Dec 2021 11:06:24: 2000000 INFO @ Fri, 10 Dec 2021 11:06:30: 6000000 INFO @ Fri, 10 Dec 2021 11:06:31: 3000000 INFO @ Fri, 10 Dec 2021 11:06:38: 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 11:06:38: 7000000 INFO @ Fri, 10 Dec 2021 11:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.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 11:06:40: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:06:40: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:06:45: 5000000 INFO @ Fri, 10 Dec 2021 11:06:47: 8000000 INFO @ Fri, 10 Dec 2021 11:06:48: 1000000 INFO @ Fri, 10 Dec 2021 11:06:52: 6000000 INFO @ Fri, 10 Dec 2021 11:06:55: 9000000 INFO @ Fri, 10 Dec 2021 11:06:57: 2000000 INFO @ Fri, 10 Dec 2021 11:06:59: 7000000 INFO @ Fri, 10 Dec 2021 11:07:04: 10000000 INFO @ Fri, 10 Dec 2021 11:07:05: 3000000 INFO @ Fri, 10 Dec 2021 11:07:06: 8000000 INFO @ Fri, 10 Dec 2021 11:07:12: 11000000 INFO @ Fri, 10 Dec 2021 11:07:13: 9000000 INFO @ Fri, 10 Dec 2021 11:07:13: 4000000 INFO @ Fri, 10 Dec 2021 11:07:20: 10000000 INFO @ Fri, 10 Dec 2021 11:07:21: 12000000 INFO @ Fri, 10 Dec 2021 11:07:21: 5000000 INFO @ Fri, 10 Dec 2021 11:07:27: 11000000 INFO @ Fri, 10 Dec 2021 11:07:29: 6000000 INFO @ Fri, 10 Dec 2021 11:07:30: 13000000 INFO @ Fri, 10 Dec 2021 11:07:34: 12000000 INFO @ Fri, 10 Dec 2021 11:07:38: 7000000 INFO @ Fri, 10 Dec 2021 11:07:38: 14000000 INFO @ Fri, 10 Dec 2021 11:07:41: 13000000 INFO @ Fri, 10 Dec 2021 11:07:46: 8000000 INFO @ Fri, 10 Dec 2021 11:07:47: 15000000 INFO @ Fri, 10 Dec 2021 11:07:49: 14000000 INFO @ Fri, 10 Dec 2021 11:07:54: 9000000 INFO @ Fri, 10 Dec 2021 11:07:55: 16000000 INFO @ Fri, 10 Dec 2021 11:07:56: 15000000 INFO @ Fri, 10 Dec 2021 11:08:02: 10000000 INFO @ Fri, 10 Dec 2021 11:08:03: 16000000 INFO @ Fri, 10 Dec 2021 11:08:04: 17000000 INFO @ Fri, 10 Dec 2021 11:08:10: 17000000 INFO @ Fri, 10 Dec 2021 11:08:10: 11000000 INFO @ Fri, 10 Dec 2021 11:08:12: 18000000 INFO @ Fri, 10 Dec 2021 11:08:18: 18000000 INFO @ Fri, 10 Dec 2021 11:08:19: 12000000 INFO @ Fri, 10 Dec 2021 11:08:21: 19000000 INFO @ Fri, 10 Dec 2021 11:08:25: 19000000 INFO @ Fri, 10 Dec 2021 11:08:28: 13000000 INFO @ Fri, 10 Dec 2021 11:08:29: 20000000 INFO @ Fri, 10 Dec 2021 11:08:32: 20000000 INFO @ Fri, 10 Dec 2021 11:08:37: 14000000 INFO @ Fri, 10 Dec 2021 11:08:37: 21000000 INFO @ Fri, 10 Dec 2021 11:08:39: 21000000 INFO @ Fri, 10 Dec 2021 11:08:45: 15000000 INFO @ Fri, 10 Dec 2021 11:08:46: 22000000 INFO @ Fri, 10 Dec 2021 11:08:47: 22000000 INFO @ Fri, 10 Dec 2021 11:08:54: 16000000 INFO @ Fri, 10 Dec 2021 11:08:54: 23000000 INFO @ Fri, 10 Dec 2021 11:08:55: 23000000 INFO @ Fri, 10 Dec 2021 11:09:02: 17000000 INFO @ Fri, 10 Dec 2021 11:09:03: 24000000 INFO @ Fri, 10 Dec 2021 11:09:03: 24000000 INFO @ Fri, 10 Dec 2021 11:09:11: 18000000 INFO @ Fri, 10 Dec 2021 11:09:11: 25000000 INFO @ Fri, 10 Dec 2021 11:09:12: 25000000 INFO @ Fri, 10 Dec 2021 11:09:19: 19000000 INFO @ Fri, 10 Dec 2021 11:09:20: 26000000 INFO @ Fri, 10 Dec 2021 11:09:20: 26000000 INFO @ Fri, 10 Dec 2021 11:09:27: 20000000 INFO @ Fri, 10 Dec 2021 11:09:28: 27000000 INFO @ Fri, 10 Dec 2021 11:09:29: 27000000 INFO @ Fri, 10 Dec 2021 11:09:36: 21000000 INFO @ Fri, 10 Dec 2021 11:09:37: 28000000 INFO @ Fri, 10 Dec 2021 11:09:37: 28000000 INFO @ Fri, 10 Dec 2021 11:09:44: 22000000 INFO @ Fri, 10 Dec 2021 11:09:45: 29000000 INFO @ Fri, 10 Dec 2021 11:09:46: 29000000 INFO @ Fri, 10 Dec 2021 11:09:53: 23000000 INFO @ Fri, 10 Dec 2021 11:09:54: 30000000 INFO @ Fri, 10 Dec 2021 11:09:54: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:10:01: 24000000 INFO @ Fri, 10 Dec 2021 11:10:02: 31000000 INFO @ Fri, 10 Dec 2021 11:10:03: 31000000 INFO @ Fri, 10 Dec 2021 11:10:10: 25000000 INFO @ Fri, 10 Dec 2021 11:10:11: 32000000 INFO @ Fri, 10 Dec 2021 11:10:11: 32000000 INFO @ Fri, 10 Dec 2021 11:10:18: 26000000 INFO @ Fri, 10 Dec 2021 11:10:19: 33000000 INFO @ Fri, 10 Dec 2021 11:10:20: 33000000 INFO @ Fri, 10 Dec 2021 11:10:27: 27000000 INFO @ Fri, 10 Dec 2021 11:10:28: 34000000 INFO @ Fri, 10 Dec 2021 11:10:29: 34000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:10:35: 28000000 INFO @ Fri, 10 Dec 2021 11:10:37: 35000000 INFO @ Fri, 10 Dec 2021 11:10:37: 35000000 INFO @ Fri, 10 Dec 2021 11:10:44: 29000000 INFO @ Fri, 10 Dec 2021 11:10:45: 36000000 INFO @ Fri, 10 Dec 2021 11:10:46: 36000000 INFO @ Fri, 10 Dec 2021 11:10:52: 30000000 INFO @ Fri, 10 Dec 2021 11:10:54: 37000000 INFO @ Fri, 10 Dec 2021 11:10:54: 37000000 INFO @ Fri, 10 Dec 2021 11:11:01: 31000000 INFO @ Fri, 10 Dec 2021 11:11:02: 38000000 INFO @ Fri, 10 Dec 2021 11:11:03: 38000000 INFO @ Fri, 10 Dec 2021 11:11:10: 32000000 INFO @ Fri, 10 Dec 2021 11:11:11: 39000000 INFO @ Fri, 10 Dec 2021 11:11:11: 39000000 INFO @ Fri, 10 Dec 2021 11:11:18: 33000000 INFO @ Fri, 10 Dec 2021 11:11:19: 40000000 INFO @ Fri, 10 Dec 2021 11:11:20: 40000000 INFO @ Fri, 10 Dec 2021 11:11:21: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:11:21: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:11:21: #1 total tags in treatment: 14191974 INFO @ Fri, 10 Dec 2021 11:11:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:11:21: #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 11:11:21: #1 tags after filtering in treatment: 8489958 INFO @ Fri, 10 Dec 2021 11:11:21: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Dec 2021 11:11:21: #1 finished! INFO @ Fri, 10 Dec 2021 11:11:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:11:21: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:11:21: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:11:21: #1 total tags in treatment: 14191974 INFO @ Fri, 10 Dec 2021 11:11:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:11:21: #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 11:11:21: #1 tags after filtering in treatment: 8489958 INFO @ Fri, 10 Dec 2021 11:11:21: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Dec 2021 11:11:21: #1 finished! INFO @ Fri, 10 Dec 2021 11:11:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:11:22: #2 number of paired peaks: 5201 INFO @ Fri, 10 Dec 2021 11:11:22: start model_add_line... INFO @ Fri, 10 Dec 2021 11:11:22: start X-correlation... INFO @ Fri, 10 Dec 2021 11:11:22: end of X-cor INFO @ Fri, 10 Dec 2021 11:11:22: #2 finished! INFO @ Fri, 10 Dec 2021 11:11:22: #2 predicted fragment length is 245 bps INFO @ Fri, 10 Dec 2021 11:11:22: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 10 Dec 2021 11:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.05_model.r WARNING @ Fri, 10 Dec 2021 11:11:22: #2 Since the d (245) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:11:22: #2 You may need to consider one of the other alternative d(s): 245 WARNING @ Fri, 10 Dec 2021 11:11:22: #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 11:11:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:11:22: #2 number of paired peaks: 5201 INFO @ Fri, 10 Dec 2021 11:11:22: start model_add_line... INFO @ Fri, 10 Dec 2021 11:11:22: start X-correlation... INFO @ Fri, 10 Dec 2021 11:11:22: end of X-cor INFO @ Fri, 10 Dec 2021 11:11:22: #2 finished! INFO @ Fri, 10 Dec 2021 11:11:22: #2 predicted fragment length is 245 bps INFO @ Fri, 10 Dec 2021 11:11:22: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 10 Dec 2021 11:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.10_model.r WARNING @ Fri, 10 Dec 2021 11:11:22: #2 Since the d (245) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:11:22: #2 You may need to consider one of the other alternative d(s): 245 WARNING @ Fri, 10 Dec 2021 11:11:22: #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 11:11:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:11:27: 34000000 INFO @ Fri, 10 Dec 2021 11:11:35: 35000000 INFO @ Fri, 10 Dec 2021 11:11:43: 36000000 INFO @ Fri, 10 Dec 2021 11:11:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:11:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:11:51: 37000000 INFO @ Fri, 10 Dec 2021 11:11:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:11:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:11:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.05_summits.bed INFO @ Fri, 10 Dec 2021 11:11:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10070 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:11:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:11:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:11:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.10_summits.bed INFO @ Fri, 10 Dec 2021 11:11:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7337 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:11:59: 38000000 INFO @ Fri, 10 Dec 2021 11:12:07: 39000000 INFO @ Fri, 10 Dec 2021 11:12:16: 40000000 INFO @ Fri, 10 Dec 2021 11:12:17: #1 tag size is determined as 150 bps INFO @ Fri, 10 Dec 2021 11:12:17: #1 tag size = 150 INFO @ Fri, 10 Dec 2021 11:12:17: #1 total tags in treatment: 14191974 INFO @ Fri, 10 Dec 2021 11:12:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:12:17: #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 11:12:17: #1 tags after filtering in treatment: 8489958 INFO @ Fri, 10 Dec 2021 11:12:17: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 10 Dec 2021 11:12:17: #1 finished! INFO @ Fri, 10 Dec 2021 11:12:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:12:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:12:18: #2 number of paired peaks: 5201 INFO @ Fri, 10 Dec 2021 11:12:18: start model_add_line... INFO @ Fri, 10 Dec 2021 11:12:18: start X-correlation... INFO @ Fri, 10 Dec 2021 11:12:18: end of X-cor INFO @ Fri, 10 Dec 2021 11:12:18: #2 finished! INFO @ Fri, 10 Dec 2021 11:12:18: #2 predicted fragment length is 245 bps INFO @ Fri, 10 Dec 2021 11:12:18: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 10 Dec 2021 11:12:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.20_model.r WARNING @ Fri, 10 Dec 2021 11:12:18: #2 Since the d (245) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:12:18: #2 You may need to consider one of the other alternative d(s): 245 WARNING @ Fri, 10 Dec 2021 11:12:18: #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 11:12:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:12:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:12:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:12:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:12:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:12:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10412049/SRX10412049.20_summits.bed INFO @ Fri, 10 Dec 2021 11:12:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4384 records, 4 fields): 5 millis CompletedMACS2peakCalling