Job ID = 14171366 SRX = SRX9304585 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 51353751 spots for SRR12837082/SRR12837082.sra Written 51353751 spots for SRR12837082/SRR12837082.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172088 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:55:45 51353751 reads; of these: 51353751 (100.00%) were paired; of these: 15627359 (30.43%) aligned concordantly 0 times 28993715 (56.46%) aligned concordantly exactly 1 time 6732677 (13.11%) aligned concordantly >1 times ---- 15627359 pairs aligned concordantly 0 times; of these: 493187 (3.16%) aligned discordantly 1 time ---- 15134172 pairs aligned 0 times concordantly or discordantly; of these: 30268344 mates make up the pairs; of these: 29293241 (96.78%) aligned 0 times 705190 (2.33%) aligned exactly 1 time 269913 (0.89%) aligned >1 times 71.48% overall alignment rate Time searching: 00:55:46 Overall time: 00:55:46 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] 20627034 / 25911835 = 0.7960 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 12:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.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 12:40:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:40:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:40:56: 1000000 INFO @ Sat, 11 Dec 2021 12:41:00: 2000000 INFO @ Sat, 11 Dec 2021 12:41:05: 3000000 INFO @ Sat, 11 Dec 2021 12:41:10: 4000000 INFO @ Sat, 11 Dec 2021 12:41:15: 5000000 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 12:41:19: 6000000 INFO @ Sat, 11 Dec 2021 12:41:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.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 12:41:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:41:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:41:24: 7000000 INFO @ Sat, 11 Dec 2021 12:41:26: 1000000 INFO @ Sat, 11 Dec 2021 12:41:30: 8000000 INFO @ Sat, 11 Dec 2021 12:41:32: 2000000 INFO @ Sat, 11 Dec 2021 12:41:35: 9000000 INFO @ Sat, 11 Dec 2021 12:41:37: 3000000 INFO @ Sat, 11 Dec 2021 12:41:40: 10000000 INFO @ Sat, 11 Dec 2021 12:41:43: 4000000 INFO @ Sat, 11 Dec 2021 12:41:46: 11000000 INFO @ Sat, 11 Dec 2021 12:41:48: 5000000 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 12:41:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.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 12:41:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:41:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:41:51: 12000000 INFO @ Sat, 11 Dec 2021 12:41:53: 6000000 INFO @ Sat, 11 Dec 2021 12:41:56: 1000000 INFO @ Sat, 11 Dec 2021 12:41:56: 13000000 INFO @ Sat, 11 Dec 2021 12:41:59: 7000000 INFO @ Sat, 11 Dec 2021 12:42:02: 2000000 INFO @ Sat, 11 Dec 2021 12:42:02: 14000000 INFO @ Sat, 11 Dec 2021 12:42:04: 8000000 INFO @ Sat, 11 Dec 2021 12:42:07: 3000000 INFO @ Sat, 11 Dec 2021 12:42:07: 15000000 INFO @ Sat, 11 Dec 2021 12:42:10: 9000000 INFO @ Sat, 11 Dec 2021 12:42:12: 4000000 INFO @ Sat, 11 Dec 2021 12:42:13: 16000000 INFO @ Sat, 11 Dec 2021 12:42:15: 10000000 INFO @ Sat, 11 Dec 2021 12:42:18: 5000000 INFO @ Sat, 11 Dec 2021 12:42:18: 17000000 INFO @ Sat, 11 Dec 2021 12:42:21: 11000000 INFO @ Sat, 11 Dec 2021 12:42:23: 6000000 INFO @ Sat, 11 Dec 2021 12:42:23: 18000000 INFO @ Sat, 11 Dec 2021 12:42:26: 12000000 INFO @ Sat, 11 Dec 2021 12:42:28: 7000000 INFO @ Sat, 11 Dec 2021 12:42:29: 19000000 INFO @ Sat, 11 Dec 2021 12:42:31: 13000000 INFO @ Sat, 11 Dec 2021 12:42:34: 8000000 INFO @ Sat, 11 Dec 2021 12:42:34: 20000000 INFO @ Sat, 11 Dec 2021 12:42:37: 14000000 INFO @ Sat, 11 Dec 2021 12:42:39: 9000000 INFO @ Sat, 11 Dec 2021 12:42:40: 21000000 INFO @ Sat, 11 Dec 2021 12:42:42: 15000000 INFO @ Sat, 11 Dec 2021 12:42:44: 10000000 INFO @ Sat, 11 Dec 2021 12:42:45: 22000000 INFO @ Sat, 11 Dec 2021 12:42:47: 16000000 INFO @ Sat, 11 Dec 2021 12:42:49: 11000000 INFO @ Sat, 11 Dec 2021 12:42:50: 23000000 INFO @ Sat, 11 Dec 2021 12:42:52: 17000000 INFO @ Sat, 11 Dec 2021 12:42:55: 12000000 INFO @ Sat, 11 Dec 2021 12:42:56: 24000000 INFO @ Sat, 11 Dec 2021 12:42:58: 18000000 INFO @ Sat, 11 Dec 2021 12:43:00: 13000000 INFO @ Sat, 11 Dec 2021 12:43:02: 25000000 INFO @ Sat, 11 Dec 2021 12:43:03: 19000000 INFO @ Sat, 11 Dec 2021 12:43:06: 14000000 INFO @ Sat, 11 Dec 2021 12:43:08: 26000000 INFO @ Sat, 11 Dec 2021 12:43:09: 20000000 INFO @ Sat, 11 Dec 2021 12:43:11: 15000000 INFO @ Sat, 11 Dec 2021 12:43:14: 27000000 INFO @ Sat, 11 Dec 2021 12:43:15: 21000000 INFO @ Sat, 11 Dec 2021 12:43:17: 16000000 INFO @ Sat, 11 Dec 2021 12:43:20: 28000000 INFO @ Sat, 11 Dec 2021 12:43:23: 22000000 INFO @ Sat, 11 Dec 2021 12:43:24: 17000000 INFO @ Sat, 11 Dec 2021 12:43:25: 29000000 INFO @ Sat, 11 Dec 2021 12:43:30: 23000000 INFO @ Sat, 11 Dec 2021 12:43:31: 18000000 INFO @ Sat, 11 Dec 2021 12:43:32: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:43:37: 24000000 INFO @ Sat, 11 Dec 2021 12:43:37: 19000000 INFO @ Sat, 11 Dec 2021 12:43:38: 31000000 INFO @ Sat, 11 Dec 2021 12:43:43: 25000000 INFO @ Sat, 11 Dec 2021 12:43:44: 32000000 INFO @ Sat, 11 Dec 2021 12:43:44: 20000000 INFO @ Sat, 11 Dec 2021 12:43:45: #1 tag size is determined as 66 bps INFO @ Sat, 11 Dec 2021 12:43:45: #1 tag size = 66 INFO @ Sat, 11 Dec 2021 12:43:45: #1 total tags in treatment: 15256180 INFO @ Sat, 11 Dec 2021 12:43:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:43:45: #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 12:43:45: #1 tags after filtering in treatment: 4913158 INFO @ Sat, 11 Dec 2021 12:43:45: #1 Redundant rate of treatment: 0.68 INFO @ Sat, 11 Dec 2021 12:43:45: #1 finished! INFO @ Sat, 11 Dec 2021 12:43:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:43:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:43:46: #2 number of paired peaks: 6668 INFO @ Sat, 11 Dec 2021 12:43:46: start model_add_line... INFO @ Sat, 11 Dec 2021 12:43:46: start X-correlation... INFO @ Sat, 11 Dec 2021 12:43:46: end of X-cor INFO @ Sat, 11 Dec 2021 12:43:46: #2 finished! INFO @ Sat, 11 Dec 2021 12:43:46: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 12:43:46: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 11 Dec 2021 12:43:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.05_model.r WARNING @ Sat, 11 Dec 2021 12:43:46: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:43:46: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 11 Dec 2021 12:43:46: #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 12:43:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:43:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:43:49: 26000000 INFO @ Sat, 11 Dec 2021 12:43:50: 21000000 INFO @ Sat, 11 Dec 2021 12:43:56: 27000000 INFO @ Sat, 11 Dec 2021 12:43:56: 22000000 INFO @ Sat, 11 Dec 2021 12:43:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:44:02: 28000000 INFO @ Sat, 11 Dec 2021 12:44:02: 23000000 INFO @ Sat, 11 Dec 2021 12:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.05_summits.bed INFO @ Sat, 11 Dec 2021 12:44:04: Done! pass1 - making usageList (14 chroms): 29 millis pass2 - checking and writing primary data (14201 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:44:07: 29000000 INFO @ Sat, 11 Dec 2021 12:44:08: 24000000 INFO @ Sat, 11 Dec 2021 12:44:13: 30000000 INFO @ Sat, 11 Dec 2021 12:44:14: 25000000 INFO @ Sat, 11 Dec 2021 12:44:18: 31000000 INFO @ Sat, 11 Dec 2021 12:44:21: 26000000 INFO @ Sat, 11 Dec 2021 12:44:23: 32000000 INFO @ Sat, 11 Dec 2021 12:44:25: #1 tag size is determined as 66 bps INFO @ Sat, 11 Dec 2021 12:44:25: #1 tag size = 66 INFO @ Sat, 11 Dec 2021 12:44:25: #1 total tags in treatment: 15256180 INFO @ Sat, 11 Dec 2021 12:44:25: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:44:25: #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 12:44:25: #1 tags after filtering in treatment: 4913158 INFO @ Sat, 11 Dec 2021 12:44:25: #1 Redundant rate of treatment: 0.68 INFO @ Sat, 11 Dec 2021 12:44:25: #1 finished! INFO @ Sat, 11 Dec 2021 12:44:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:44:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:44:26: #2 number of paired peaks: 6668 INFO @ Sat, 11 Dec 2021 12:44:26: start model_add_line... INFO @ Sat, 11 Dec 2021 12:44:26: start X-correlation... INFO @ Sat, 11 Dec 2021 12:44:26: end of X-cor INFO @ Sat, 11 Dec 2021 12:44:26: #2 finished! INFO @ Sat, 11 Dec 2021 12:44:26: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 12:44:26: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 11 Dec 2021 12:44:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.10_model.r WARNING @ Sat, 11 Dec 2021 12:44:26: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:44:26: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 11 Dec 2021 12:44:26: #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 12:44:26: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:44:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:44:27: 27000000 INFO @ Sat, 11 Dec 2021 12:44:33: 28000000 INFO @ Sat, 11 Dec 2021 12:44:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:44:39: 29000000 INFO @ Sat, 11 Dec 2021 12:44:45: 30000000 INFO @ Sat, 11 Dec 2021 12:44:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:44:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:44:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.10_summits.bed INFO @ Sat, 11 Dec 2021 12:44:45: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (9571 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:44:50: 31000000 INFO @ Sat, 11 Dec 2021 12:44:56: 32000000 INFO @ Sat, 11 Dec 2021 12:44:57: #1 tag size is determined as 66 bps INFO @ Sat, 11 Dec 2021 12:44:57: #1 tag size = 66 INFO @ Sat, 11 Dec 2021 12:44:57: #1 total tags in treatment: 15256180 INFO @ Sat, 11 Dec 2021 12:44:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:44:57: #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 12:44:58: #1 tags after filtering in treatment: 4913158 INFO @ Sat, 11 Dec 2021 12:44:58: #1 Redundant rate of treatment: 0.68 INFO @ Sat, 11 Dec 2021 12:44:58: #1 finished! INFO @ Sat, 11 Dec 2021 12:44:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:44:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:44:58: #2 number of paired peaks: 6668 INFO @ Sat, 11 Dec 2021 12:44:58: start model_add_line... INFO @ Sat, 11 Dec 2021 12:44:58: start X-correlation... INFO @ Sat, 11 Dec 2021 12:44:58: end of X-cor INFO @ Sat, 11 Dec 2021 12:44:58: #2 finished! INFO @ Sat, 11 Dec 2021 12:44:58: #2 predicted fragment length is 100 bps INFO @ Sat, 11 Dec 2021 12:44:58: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 11 Dec 2021 12:44:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.20_model.r WARNING @ Sat, 11 Dec 2021 12:44:58: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:44:58: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 11 Dec 2021 12:44:58: #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 12:44:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:44:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:45:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:45:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:45:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:45:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304585/SRX9304585.20_summits.bed INFO @ Sat, 11 Dec 2021 12:45:16: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (4432 records, 4 fields): 6 millis CompletedMACS2peakCalling