Job ID = 14171362 SRX = SRX9304582 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 49907675 spots for SRR12837079/SRR12837079.sra Written 49907675 spots for SRR12837079/SRR12837079.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172061 ("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: 00:46:55 49907675 reads; of these: 49907675 (100.00%) were paired; of these: 15982731 (32.02%) aligned concordantly 0 times 28818242 (57.74%) aligned concordantly exactly 1 time 5106702 (10.23%) aligned concordantly >1 times ---- 15982731 pairs aligned concordantly 0 times; of these: 456055 (2.85%) aligned discordantly 1 time ---- 15526676 pairs aligned 0 times concordantly or discordantly; of these: 31053352 mates make up the pairs; of these: 30151343 (97.10%) aligned 0 times 667964 (2.15%) aligned exactly 1 time 234045 (0.75%) aligned >1 times 69.79% overall alignment rate Time searching: 00:46:55 Overall time: 00:46:55 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] 15069889 / 22399265 = 0.6728 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 12:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.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 12:31:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:31:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:31:43: 1000000 INFO @ Sat, 11 Dec 2021 12:31:48: 2000000 INFO @ Sat, 11 Dec 2021 12:31:54: 3000000 INFO @ Sat, 11 Dec 2021 12:32:00: 4000000 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 12:32:06: 5000000 INFO @ Sat, 11 Dec 2021 12:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.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 12:32:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:32:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:32:12: 6000000 INFO @ Sat, 11 Dec 2021 12:32:13: 1000000 INFO @ Sat, 11 Dec 2021 12:32:19: 7000000 INFO @ Sat, 11 Dec 2021 12:32:20: 2000000 INFO @ Sat, 11 Dec 2021 12:32:25: 8000000 INFO @ Sat, 11 Dec 2021 12:32:27: 3000000 INFO @ Sat, 11 Dec 2021 12:32:31: 9000000 INFO @ Sat, 11 Dec 2021 12:32:34: 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 @ Sat, 11 Dec 2021 12:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.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 12:32:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:32:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:32:38: 10000000 INFO @ Sat, 11 Dec 2021 12:32:41: 5000000 INFO @ Sat, 11 Dec 2021 12:32:44: 1000000 INFO @ Sat, 11 Dec 2021 12:32:45: 11000000 INFO @ Sat, 11 Dec 2021 12:32:49: 6000000 INFO @ Sat, 11 Dec 2021 12:32:52: 2000000 INFO @ Sat, 11 Dec 2021 12:32:52: 12000000 INFO @ Sat, 11 Dec 2021 12:32:57: 7000000 INFO @ Sat, 11 Dec 2021 12:33:00: 3000000 INFO @ Sat, 11 Dec 2021 12:33:00: 13000000 INFO @ Sat, 11 Dec 2021 12:33:04: 8000000 INFO @ Sat, 11 Dec 2021 12:33:07: 14000000 INFO @ Sat, 11 Dec 2021 12:33:07: 4000000 INFO @ Sat, 11 Dec 2021 12:33:12: 9000000 INFO @ Sat, 11 Dec 2021 12:33:14: 15000000 INFO @ Sat, 11 Dec 2021 12:33:15: 5000000 INFO @ Sat, 11 Dec 2021 12:33:20: 10000000 INFO @ Sat, 11 Dec 2021 12:33:21: 16000000 INFO @ Sat, 11 Dec 2021 12:33:23: 6000000 INFO @ Sat, 11 Dec 2021 12:33:28: 11000000 INFO @ Sat, 11 Dec 2021 12:33:29: 17000000 INFO @ Sat, 11 Dec 2021 12:33:31: 7000000 INFO @ Sat, 11 Dec 2021 12:33:35: 12000000 INFO @ Sat, 11 Dec 2021 12:33:36: 18000000 INFO @ Sat, 11 Dec 2021 12:33:39: 8000000 INFO @ Sat, 11 Dec 2021 12:33:43: 13000000 INFO @ Sat, 11 Dec 2021 12:33:43: 19000000 INFO @ Sat, 11 Dec 2021 12:33:47: 9000000 INFO @ Sat, 11 Dec 2021 12:33:50: 14000000 INFO @ Sat, 11 Dec 2021 12:33:51: 20000000 INFO @ Sat, 11 Dec 2021 12:33:55: 10000000 INFO @ Sat, 11 Dec 2021 12:33:58: 15000000 INFO @ Sat, 11 Dec 2021 12:33:58: 21000000 INFO @ Sat, 11 Dec 2021 12:34:03: 11000000 INFO @ Sat, 11 Dec 2021 12:34:05: 16000000 INFO @ Sat, 11 Dec 2021 12:34:05: 22000000 INFO @ Sat, 11 Dec 2021 12:34:10: 12000000 INFO @ Sat, 11 Dec 2021 12:34:12: 23000000 INFO @ Sat, 11 Dec 2021 12:34:13: 17000000 INFO @ Sat, 11 Dec 2021 12:34:18: 13000000 INFO @ Sat, 11 Dec 2021 12:34:20: 24000000 INFO @ Sat, 11 Dec 2021 12:34:20: 18000000 INFO @ Sat, 11 Dec 2021 12:34:26: 14000000 INFO @ Sat, 11 Dec 2021 12:34:27: 25000000 INFO @ Sat, 11 Dec 2021 12:34:27: 19000000 INFO @ Sat, 11 Dec 2021 12:34:34: 26000000 INFO @ Sat, 11 Dec 2021 12:34:34: 15000000 INFO @ Sat, 11 Dec 2021 12:34:35: 20000000 INFO @ Sat, 11 Dec 2021 12:34:42: 27000000 INFO @ Sat, 11 Dec 2021 12:34:42: 21000000 INFO @ Sat, 11 Dec 2021 12:34:43: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:34:49: 28000000 INFO @ Sat, 11 Dec 2021 12:34:50: 22000000 INFO @ Sat, 11 Dec 2021 12:34:51: 17000000 INFO @ Sat, 11 Dec 2021 12:34:56: 29000000 INFO @ Sat, 11 Dec 2021 12:34:57: 23000000 INFO @ Sat, 11 Dec 2021 12:34:59: 18000000 INFO @ Sat, 11 Dec 2021 12:35:03: 30000000 INFO @ Sat, 11 Dec 2021 12:35:05: 24000000 INFO @ Sat, 11 Dec 2021 12:35:07: 19000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:35:11: 31000000 INFO @ Sat, 11 Dec 2021 12:35:12: 25000000 INFO @ Sat, 11 Dec 2021 12:35:16: 20000000 INFO @ Sat, 11 Dec 2021 12:35:18: 32000000 INFO @ Sat, 11 Dec 2021 12:35:20: 26000000 INFO @ Sat, 11 Dec 2021 12:35:24: 21000000 INFO @ Sat, 11 Dec 2021 12:35:26: 33000000 INFO @ Sat, 11 Dec 2021 12:35:27: 27000000 INFO @ Sat, 11 Dec 2021 12:35:32: 22000000 INFO @ Sat, 11 Dec 2021 12:35:34: 34000000 INFO @ Sat, 11 Dec 2021 12:35:34: 28000000 INFO @ Sat, 11 Dec 2021 12:35:40: 23000000 INFO @ Sat, 11 Dec 2021 12:35:42: 35000000 INFO @ Sat, 11 Dec 2021 12:35:42: 29000000 INFO @ Sat, 11 Dec 2021 12:35:49: 24000000 INFO @ Sat, 11 Dec 2021 12:35:49: 36000000 INFO @ Sat, 11 Dec 2021 12:35:50: 30000000 INFO @ Sat, 11 Dec 2021 12:35:56: 37000000 INFO @ Sat, 11 Dec 2021 12:35:57: 25000000 INFO @ Sat, 11 Dec 2021 12:35:57: 31000000 INFO @ Sat, 11 Dec 2021 12:36:04: 38000000 INFO @ Sat, 11 Dec 2021 12:36:05: 26000000 INFO @ Sat, 11 Dec 2021 12:36:05: 32000000 INFO @ Sat, 11 Dec 2021 12:36:11: 39000000 INFO @ Sat, 11 Dec 2021 12:36:13: 33000000 INFO @ Sat, 11 Dec 2021 12:36:13: 27000000 INFO @ Sat, 11 Dec 2021 12:36:15: #1 tag size is determined as 71 bps INFO @ Sat, 11 Dec 2021 12:36:15: #1 tag size = 71 INFO @ Sat, 11 Dec 2021 12:36:15: #1 total tags in treatment: 18946417 INFO @ Sat, 11 Dec 2021 12:36:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:36:15: #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 12:36:15: #1 tags after filtering in treatment: 7322244 INFO @ Sat, 11 Dec 2021 12:36:15: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 11 Dec 2021 12:36:15: #1 finished! INFO @ Sat, 11 Dec 2021 12:36:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:36:16: #2 number of paired peaks: 4762 INFO @ Sat, 11 Dec 2021 12:36:16: start model_add_line... INFO @ Sat, 11 Dec 2021 12:36:16: start X-correlation... INFO @ Sat, 11 Dec 2021 12:36:16: end of X-cor INFO @ Sat, 11 Dec 2021 12:36:16: #2 finished! INFO @ Sat, 11 Dec 2021 12:36:16: #2 predicted fragment length is 66 bps INFO @ Sat, 11 Dec 2021 12:36:16: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 11 Dec 2021 12:36:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.05_model.r WARNING @ Sat, 11 Dec 2021 12:36:16: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:36:16: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 11 Dec 2021 12:36:16: #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 12:36:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:36:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:36:21: 34000000 INFO @ Sat, 11 Dec 2021 12:36:21: 28000000 INFO @ Sat, 11 Dec 2021 12:36:28: 35000000 INFO @ Sat, 11 Dec 2021 12:36:30: 29000000 INFO @ Sat, 11 Dec 2021 12:36:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:36:36: 36000000 INFO @ Sat, 11 Dec 2021 12:36:38: 30000000 INFO @ Sat, 11 Dec 2021 12:36:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:36:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:36:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.05_summits.bed INFO @ Sat, 11 Dec 2021 12:36:39: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (19356 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:36:43: 37000000 INFO @ Sat, 11 Dec 2021 12:36:47: 31000000 INFO @ Sat, 11 Dec 2021 12:36:50: 38000000 INFO @ Sat, 11 Dec 2021 12:36:56: 32000000 INFO @ Sat, 11 Dec 2021 12:36:58: 39000000 INFO @ Sat, 11 Dec 2021 12:37:02: #1 tag size is determined as 71 bps INFO @ Sat, 11 Dec 2021 12:37:02: #1 tag size = 71 INFO @ Sat, 11 Dec 2021 12:37:02: #1 total tags in treatment: 18946417 INFO @ Sat, 11 Dec 2021 12:37:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:37:02: #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 12:37:02: #1 tags after filtering in treatment: 7322244 INFO @ Sat, 11 Dec 2021 12:37:02: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 11 Dec 2021 12:37:02: #1 finished! INFO @ Sat, 11 Dec 2021 12:37:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:37:03: #2 number of paired peaks: 4762 INFO @ Sat, 11 Dec 2021 12:37:03: start model_add_line... INFO @ Sat, 11 Dec 2021 12:37:03: start X-correlation... INFO @ Sat, 11 Dec 2021 12:37:03: end of X-cor INFO @ Sat, 11 Dec 2021 12:37:03: #2 finished! INFO @ Sat, 11 Dec 2021 12:37:03: #2 predicted fragment length is 66 bps INFO @ Sat, 11 Dec 2021 12:37:03: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 11 Dec 2021 12:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.10_model.r WARNING @ Sat, 11 Dec 2021 12:37:03: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:37:03: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 11 Dec 2021 12:37:03: #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 12:37:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:37:05: 33000000 INFO @ Sat, 11 Dec 2021 12:37:13: 34000000 INFO @ Sat, 11 Dec 2021 12:37:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:37:21: 35000000 INFO @ Sat, 11 Dec 2021 12:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:37:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:37:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.10_summits.bed INFO @ Sat, 11 Dec 2021 12:37:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11435 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:37:29: 36000000 INFO @ Sat, 11 Dec 2021 12:37:36: 37000000 INFO @ Sat, 11 Dec 2021 12:37:44: 38000000 INFO @ Sat, 11 Dec 2021 12:37:52: 39000000 INFO @ Sat, 11 Dec 2021 12:37:56: #1 tag size is determined as 71 bps INFO @ Sat, 11 Dec 2021 12:37:56: #1 tag size = 71 INFO @ Sat, 11 Dec 2021 12:37:56: #1 total tags in treatment: 18946417 INFO @ Sat, 11 Dec 2021 12:37:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:37:56: #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 12:37:56: #1 tags after filtering in treatment: 7322244 INFO @ Sat, 11 Dec 2021 12:37:56: #1 Redundant rate of treatment: 0.61 INFO @ Sat, 11 Dec 2021 12:37:56: #1 finished! INFO @ Sat, 11 Dec 2021 12:37:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:37:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:37:57: #2 number of paired peaks: 4762 INFO @ Sat, 11 Dec 2021 12:37:57: start model_add_line... INFO @ Sat, 11 Dec 2021 12:37:57: start X-correlation... INFO @ Sat, 11 Dec 2021 12:37:57: end of X-cor INFO @ Sat, 11 Dec 2021 12:37:57: #2 finished! INFO @ Sat, 11 Dec 2021 12:37:57: #2 predicted fragment length is 66 bps INFO @ Sat, 11 Dec 2021 12:37:57: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 11 Dec 2021 12:37:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.20_model.r WARNING @ Sat, 11 Dec 2021 12:37:57: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:37:57: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 11 Dec 2021 12:37:57: #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 12:37:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:37:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:38:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304582/SRX9304582.20_summits.bed INFO @ Sat, 11 Dec 2021 12:38:19: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (3437 records, 4 fields): 4 millis CompletedMACS2peakCalling