Job ID = 16439371 SRX = SRX14232181 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18761102 spots for SRR18080637/SRR18080637.sra Written 18761102 spots for SRR18080637/SRR18080637.sra fastq に変換しました。 bowtie でマッピング中... Your job 16441004 ("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: 03:21:09 18761102 reads; of these: 18761102 (100.00%) were paired; of these: 5456181 (29.08%) aligned concordantly 0 times 7949555 (42.37%) aligned concordantly exactly 1 time 5355366 (28.55%) aligned concordantly >1 times ---- 5456181 pairs aligned concordantly 0 times; of these: 1377746 (25.25%) aligned discordantly 1 time ---- 4078435 pairs aligned 0 times concordantly or discordantly; of these: 8156870 mates make up the pairs; of these: 5602679 (68.69%) aligned 0 times 391165 (4.80%) aligned exactly 1 time 2163026 (26.52%) aligned >1 times 85.07% overall alignment rate Time searching: 03:21:09 Overall time: 03:21:09 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] 2787117 / 14545530 = 0.1916 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.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 @ Tue, 02 Aug 2022 18:41:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:41:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:41:24: 1000000 INFO @ Tue, 02 Aug 2022 18:41:32: 2000000 INFO @ Tue, 02 Aug 2022 18:41:39: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:41:46: 4000000 INFO @ Tue, 02 Aug 2022 18:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.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 @ Tue, 02 Aug 2022 18:41:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:41:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:41:54: 5000000 INFO @ Tue, 02 Aug 2022 18:41:54: 1000000 INFO @ Tue, 02 Aug 2022 18:42:02: 2000000 INFO @ Tue, 02 Aug 2022 18:42:02: 6000000 INFO @ Tue, 02 Aug 2022 18:42:10: 3000000 INFO @ Tue, 02 Aug 2022 18:42:11: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 18:42:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.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 @ Tue, 02 Aug 2022 18:42:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:42:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:42:18: 4000000 INFO @ Tue, 02 Aug 2022 18:42:19: 8000000 INFO @ Tue, 02 Aug 2022 18:42:24: 1000000 INFO @ Tue, 02 Aug 2022 18:42:26: 5000000 INFO @ Tue, 02 Aug 2022 18:42:28: 9000000 INFO @ Tue, 02 Aug 2022 18:42:32: 2000000 INFO @ Tue, 02 Aug 2022 18:42:34: 6000000 INFO @ Tue, 02 Aug 2022 18:42:37: 10000000 INFO @ Tue, 02 Aug 2022 18:42:40: 3000000 INFO @ Tue, 02 Aug 2022 18:42:42: 7000000 INFO @ Tue, 02 Aug 2022 18:42:46: 11000000 INFO @ Tue, 02 Aug 2022 18:42:48: 4000000 INFO @ Tue, 02 Aug 2022 18:42:51: 8000000 INFO @ Tue, 02 Aug 2022 18:42:54: 12000000 INFO @ Tue, 02 Aug 2022 18:42:56: 5000000 INFO @ Tue, 02 Aug 2022 18:42:59: 9000000 INFO @ Tue, 02 Aug 2022 18:43:04: 13000000 INFO @ Tue, 02 Aug 2022 18:43:04: 6000000 INFO @ Tue, 02 Aug 2022 18:43:08: 10000000 INFO @ Tue, 02 Aug 2022 18:43:12: 7000000 INFO @ Tue, 02 Aug 2022 18:43:12: 14000000 INFO @ Tue, 02 Aug 2022 18:43:16: 11000000 INFO @ Tue, 02 Aug 2022 18:43:20: 8000000 INFO @ Tue, 02 Aug 2022 18:43:21: 15000000 INFO @ Tue, 02 Aug 2022 18:43:25: 12000000 INFO @ Tue, 02 Aug 2022 18:43:28: 9000000 INFO @ Tue, 02 Aug 2022 18:43:29: 16000000 INFO @ Tue, 02 Aug 2022 18:43:33: 13000000 INFO @ Tue, 02 Aug 2022 18:43:36: 10000000 INFO @ Tue, 02 Aug 2022 18:43:37: 17000000 INFO @ Tue, 02 Aug 2022 18:43:41: 14000000 INFO @ Tue, 02 Aug 2022 18:43:44: 11000000 INFO @ Tue, 02 Aug 2022 18:43:46: 18000000 INFO @ Tue, 02 Aug 2022 18:43:49: 15000000 INFO @ Tue, 02 Aug 2022 18:43:52: 12000000 INFO @ Tue, 02 Aug 2022 18:43:53: 19000000 INFO @ Tue, 02 Aug 2022 18:43:57: 16000000 INFO @ Tue, 02 Aug 2022 18:44:01: 13000000 INFO @ Tue, 02 Aug 2022 18:44:01: 20000000 INFO @ Tue, 02 Aug 2022 18:44:05: 17000000 INFO @ Tue, 02 Aug 2022 18:44:09: 14000000 INFO @ Tue, 02 Aug 2022 18:44:09: 21000000 INFO @ Tue, 02 Aug 2022 18:44:12: 18000000 INFO @ Tue, 02 Aug 2022 18:44:17: 15000000 INFO @ Tue, 02 Aug 2022 18:44:18: 22000000 INFO @ Tue, 02 Aug 2022 18:44:20: 19000000 INFO @ Tue, 02 Aug 2022 18:44:24: 16000000 INFO @ Tue, 02 Aug 2022 18:44:26: 23000000 INFO @ Tue, 02 Aug 2022 18:44:28: 20000000 INFO @ Tue, 02 Aug 2022 18:44:33: 17000000 INFO @ Tue, 02 Aug 2022 18:44:35: 24000000 INFO @ Tue, 02 Aug 2022 18:44:36: 21000000 INFO @ Tue, 02 Aug 2022 18:44:41: 18000000 INFO @ Tue, 02 Aug 2022 18:44:43: 25000000 INFO @ Tue, 02 Aug 2022 18:44:44: 22000000 INFO @ Tue, 02 Aug 2022 18:44:50: 19000000 INFO @ Tue, 02 Aug 2022 18:44:51: 26000000 INFO @ Tue, 02 Aug 2022 18:44:53: 23000000 INFO @ Tue, 02 Aug 2022 18:44:55: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:44:55: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:44:55: #1 total tags in treatment: 10758648 INFO @ Tue, 02 Aug 2022 18:44:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:44:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:44:55: #1 tags after filtering in treatment: 8329802 INFO @ Tue, 02 Aug 2022 18:44:55: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 18:44:55: #1 finished! INFO @ Tue, 02 Aug 2022 18:44:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:44:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:44:56: #2 number of paired peaks: 2431 INFO @ Tue, 02 Aug 2022 18:44:56: start model_add_line... INFO @ Tue, 02 Aug 2022 18:44:56: start X-correlation... INFO @ Tue, 02 Aug 2022 18:44:56: end of X-cor INFO @ Tue, 02 Aug 2022 18:44:56: #2 finished! INFO @ Tue, 02 Aug 2022 18:44:56: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 18:44:56: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 02 Aug 2022 18:44:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.05_model.r WARNING @ Tue, 02 Aug 2022 18:44:56: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:44:56: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Tue, 02 Aug 2022 18:44:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:44:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:44:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:44:58: 20000000 INFO @ Tue, 02 Aug 2022 18:45:00: 24000000 INFO @ Tue, 02 Aug 2022 18:45:07: 21000000 INFO @ Tue, 02 Aug 2022 18:45:08: 25000000 INFO @ Tue, 02 Aug 2022 18:45:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:45:15: 22000000 INFO @ Tue, 02 Aug 2022 18:45:16: 26000000 INFO @ Tue, 02 Aug 2022 18:45:19: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:45:19: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:45:19: #1 total tags in treatment: 10758648 INFO @ Tue, 02 Aug 2022 18:45:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:45:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:45:19: #1 tags after filtering in treatment: 8329802 INFO @ Tue, 02 Aug 2022 18:45:19: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 18:45:19: #1 finished! INFO @ Tue, 02 Aug 2022 18:45:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:45:19: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:45:20: #2 number of paired peaks: 2431 INFO @ Tue, 02 Aug 2022 18:45:20: start model_add_line... INFO @ Tue, 02 Aug 2022 18:45:20: start X-correlation... INFO @ Tue, 02 Aug 2022 18:45:20: end of X-cor INFO @ Tue, 02 Aug 2022 18:45:20: #2 finished! INFO @ Tue, 02 Aug 2022 18:45:20: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 18:45:20: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 02 Aug 2022 18:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.10_model.r WARNING @ Tue, 02 Aug 2022 18:45:20: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:45:20: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Tue, 02 Aug 2022 18:45:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:45:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.05_summits.bed INFO @ Tue, 02 Aug 2022 18:45:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5065 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:45:24: 23000000 INFO @ Tue, 02 Aug 2022 18:45:33: 24000000 INFO @ Tue, 02 Aug 2022 18:45:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:45:42: 25000000 INFO @ Tue, 02 Aug 2022 18:45:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:45:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:45:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.10_summits.bed INFO @ Tue, 02 Aug 2022 18:45:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3745 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:45:50: 26000000 INFO @ Tue, 02 Aug 2022 18:45:53: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 18:45:53: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 18:45:53: #1 total tags in treatment: 10758648 INFO @ Tue, 02 Aug 2022 18:45:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:45:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 18:45:54: #1 tags after filtering in treatment: 8329802 INFO @ Tue, 02 Aug 2022 18:45:54: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 02 Aug 2022 18:45:54: #1 finished! INFO @ Tue, 02 Aug 2022 18:45:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:45:54: #2 number of paired peaks: 2431 INFO @ Tue, 02 Aug 2022 18:45:54: start model_add_line... INFO @ Tue, 02 Aug 2022 18:45:55: start X-correlation... INFO @ Tue, 02 Aug 2022 18:45:55: end of X-cor INFO @ Tue, 02 Aug 2022 18:45:55: #2 finished! INFO @ Tue, 02 Aug 2022 18:45:55: #2 predicted fragment length is 192 bps INFO @ Tue, 02 Aug 2022 18:45:55: #2 alternative fragment length(s) may be 192 bps INFO @ Tue, 02 Aug 2022 18:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.20_model.r WARNING @ Tue, 02 Aug 2022 18:45:55: #2 Since the d (192) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:45:55: #2 You may need to consider one of the other alternative d(s): 192 WARNING @ Tue, 02 Aug 2022 18:45:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 18:45:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:45:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:46:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14232181/SRX14232181.20_summits.bed INFO @ Tue, 02 Aug 2022 18:46:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2978 records, 4 fields): 24 millis CompletedMACS2peakCalling