Job ID = 16440038 SRX = SRX10855765 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24789622 spots for SRR14509952/SRR14509952.sra Written 24789622 spots for SRR14509952/SRR14509952.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440750 ("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: 00:58:56 24789622 reads; of these: 24789622 (100.00%) were paired; of these: 1904729 (7.68%) aligned concordantly 0 times 16321179 (65.84%) aligned concordantly exactly 1 time 6563714 (26.48%) aligned concordantly >1 times ---- 1904729 pairs aligned concordantly 0 times; of these: 296417 (15.56%) aligned discordantly 1 time ---- 1608312 pairs aligned 0 times concordantly or discordantly; of these: 3216624 mates make up the pairs; of these: 2416570 (75.13%) aligned 0 times 531782 (16.53%) aligned exactly 1 time 268272 (8.34%) aligned >1 times 95.13% overall alignment rate Time searching: 00:58:56 Overall time: 00:58:56 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 20 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] 3883188 / 23117057 = 0.1680 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 18:00:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.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 18:00:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:00:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:00:26: 1000000 INFO @ Tue, 02 Aug 2022 18:00:32: 2000000 INFO @ Tue, 02 Aug 2022 18:00:38: 3000000 INFO @ Tue, 02 Aug 2022 18:00:45: 4000000 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 18:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.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 18:00:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:00:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:00:52: 5000000 INFO @ Tue, 02 Aug 2022 18:00:58: 1000000 INFO @ Tue, 02 Aug 2022 18:01:00: 6000000 INFO @ Tue, 02 Aug 2022 18:01:07: 2000000 INFO @ Tue, 02 Aug 2022 18:01:08: 7000000 INFO @ Tue, 02 Aug 2022 18:01:16: 8000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 18:01:17: 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 18:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.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 18:01:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 18:01:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 18:01:24: 9000000 INFO @ Tue, 02 Aug 2022 18:01:26: 4000000 INFO @ Tue, 02 Aug 2022 18:01:27: 1000000 INFO @ Tue, 02 Aug 2022 18:01:32: 10000000 INFO @ Tue, 02 Aug 2022 18:01:36: 2000000 INFO @ Tue, 02 Aug 2022 18:01:36: 5000000 INFO @ Tue, 02 Aug 2022 18:01:41: 11000000 INFO @ Tue, 02 Aug 2022 18:01:44: 3000000 INFO @ Tue, 02 Aug 2022 18:01:45: 6000000 INFO @ Tue, 02 Aug 2022 18:01:49: 12000000 INFO @ Tue, 02 Aug 2022 18:01:53: 4000000 INFO @ Tue, 02 Aug 2022 18:01:55: 7000000 INFO @ Tue, 02 Aug 2022 18:01:58: 13000000 INFO @ Tue, 02 Aug 2022 18:02:01: 5000000 INFO @ Tue, 02 Aug 2022 18:02:04: 8000000 INFO @ Tue, 02 Aug 2022 18:02:06: 14000000 INFO @ Tue, 02 Aug 2022 18:02:09: 6000000 INFO @ Tue, 02 Aug 2022 18:02:13: 9000000 INFO @ Tue, 02 Aug 2022 18:02:14: 15000000 INFO @ Tue, 02 Aug 2022 18:02:18: 7000000 INFO @ Tue, 02 Aug 2022 18:02:22: 10000000 INFO @ Tue, 02 Aug 2022 18:02:23: 16000000 INFO @ Tue, 02 Aug 2022 18:02:26: 8000000 INFO @ Tue, 02 Aug 2022 18:02:31: 11000000 INFO @ Tue, 02 Aug 2022 18:02:31: 17000000 INFO @ Tue, 02 Aug 2022 18:02:35: 9000000 INFO @ Tue, 02 Aug 2022 18:02:40: 18000000 INFO @ Tue, 02 Aug 2022 18:02:40: 12000000 INFO @ Tue, 02 Aug 2022 18:02:43: 10000000 INFO @ Tue, 02 Aug 2022 18:02:48: 19000000 INFO @ Tue, 02 Aug 2022 18:02:49: 13000000 INFO @ Tue, 02 Aug 2022 18:02:52: 11000000 INFO @ Tue, 02 Aug 2022 18:02:56: 20000000 INFO @ Tue, 02 Aug 2022 18:02:57: 14000000 INFO @ Tue, 02 Aug 2022 18:03:00: 12000000 INFO @ Tue, 02 Aug 2022 18:03:05: 21000000 INFO @ Tue, 02 Aug 2022 18:03:06: 15000000 INFO @ Tue, 02 Aug 2022 18:03:08: 13000000 INFO @ Tue, 02 Aug 2022 18:03:13: 22000000 INFO @ Tue, 02 Aug 2022 18:03:15: 16000000 INFO @ Tue, 02 Aug 2022 18:03:17: 14000000 INFO @ Tue, 02 Aug 2022 18:03:21: 23000000 INFO @ Tue, 02 Aug 2022 18:03:24: 17000000 INFO @ Tue, 02 Aug 2022 18:03:25: 15000000 INFO @ Tue, 02 Aug 2022 18:03:30: 24000000 INFO @ Tue, 02 Aug 2022 18:03:32: 18000000 INFO @ Tue, 02 Aug 2022 18:03:34: 16000000 INFO @ Tue, 02 Aug 2022 18:03:38: 25000000 INFO @ Tue, 02 Aug 2022 18:03:41: 19000000 INFO @ Tue, 02 Aug 2022 18:03:42: 17000000 INFO @ Tue, 02 Aug 2022 18:03:47: 26000000 INFO @ Tue, 02 Aug 2022 18:03:50: 20000000 INFO @ Tue, 02 Aug 2022 18:03:51: 18000000 INFO @ Tue, 02 Aug 2022 18:03:55: 27000000 INFO @ Tue, 02 Aug 2022 18:03:59: 19000000 INFO @ Tue, 02 Aug 2022 18:03:59: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 18:04:04: 28000000 INFO @ Tue, 02 Aug 2022 18:04:08: 20000000 INFO @ Tue, 02 Aug 2022 18:04:08: 22000000 INFO @ Tue, 02 Aug 2022 18:04:12: 29000000 INFO @ Tue, 02 Aug 2022 18:04:16: 21000000 INFO @ Tue, 02 Aug 2022 18:04:17: 23000000 INFO @ Tue, 02 Aug 2022 18:04:21: 30000000 INFO @ Tue, 02 Aug 2022 18:04:25: 22000000 INFO @ Tue, 02 Aug 2022 18:04:26: 24000000 INFO @ Tue, 02 Aug 2022 18:04:29: 31000000 INFO @ Tue, 02 Aug 2022 18:04:33: 23000000 INFO @ Tue, 02 Aug 2022 18:04:36: 25000000 INFO @ Tue, 02 Aug 2022 18:04:38: 32000000 INFO @ Tue, 02 Aug 2022 18:04:41: 24000000 INFO @ Tue, 02 Aug 2022 18:04:45: 26000000 INFO @ Tue, 02 Aug 2022 18:04:46: 33000000 INFO @ Tue, 02 Aug 2022 18:04:50: 25000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 18:04:53: 27000000 INFO @ Tue, 02 Aug 2022 18:04:55: 34000000 INFO @ Tue, 02 Aug 2022 18:04:58: 26000000 INFO @ Tue, 02 Aug 2022 18:05:02: 28000000 INFO @ Tue, 02 Aug 2022 18:05:03: 35000000 INFO @ Tue, 02 Aug 2022 18:05:07: 27000000 INFO @ Tue, 02 Aug 2022 18:05:11: 29000000 INFO @ Tue, 02 Aug 2022 18:05:12: 36000000 INFO @ Tue, 02 Aug 2022 18:05:15: 28000000 INFO @ Tue, 02 Aug 2022 18:05:20: 30000000 INFO @ Tue, 02 Aug 2022 18:05:20: 37000000 INFO @ Tue, 02 Aug 2022 18:05:24: 29000000 INFO @ Tue, 02 Aug 2022 18:05:28: 38000000 INFO @ Tue, 02 Aug 2022 18:05:29: 31000000 INFO @ Tue, 02 Aug 2022 18:05:32: 30000000 INFO @ Tue, 02 Aug 2022 18:05:37: 39000000 INFO @ Tue, 02 Aug 2022 18:05:37: 32000000 INFO @ Tue, 02 Aug 2022 18:05:40: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 18:05:40: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 18:05:40: #1 total tags in treatment: 19017291 INFO @ Tue, 02 Aug 2022 18:05:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:05:40: #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 18:05:41: 31000000 INFO @ Tue, 02 Aug 2022 18:05:41: #1 tags after filtering in treatment: 12774341 INFO @ Tue, 02 Aug 2022 18:05:41: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 18:05:41: #1 finished! INFO @ Tue, 02 Aug 2022 18:05:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:05:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:05:42: #2 number of paired peaks: 2932 INFO @ Tue, 02 Aug 2022 18:05:42: start model_add_line... INFO @ Tue, 02 Aug 2022 18:05:42: start X-correlation... INFO @ Tue, 02 Aug 2022 18:05:42: end of X-cor INFO @ Tue, 02 Aug 2022 18:05:42: #2 finished! INFO @ Tue, 02 Aug 2022 18:05:42: #2 predicted fragment length is 179 bps INFO @ Tue, 02 Aug 2022 18:05:42: #2 alternative fragment length(s) may be 0,15,179,295,328 bps INFO @ Tue, 02 Aug 2022 18:05:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.05_model.r WARNING @ Tue, 02 Aug 2022 18:05:42: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:05:42: #2 You may need to consider one of the other alternative d(s): 0,15,179,295,328 WARNING @ Tue, 02 Aug 2022 18:05:42: #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 18:05:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:05:46: 33000000 INFO @ Tue, 02 Aug 2022 18:05:49: 32000000 INFO @ Tue, 02 Aug 2022 18:05:55: 34000000 INFO @ Tue, 02 Aug 2022 18:05:57: 33000000 INFO @ Tue, 02 Aug 2022 18:06:04: 35000000 INFO @ Tue, 02 Aug 2022 18:06:05: 34000000 INFO @ Tue, 02 Aug 2022 18:06:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:06:13: 36000000 INFO @ Tue, 02 Aug 2022 18:06:13: 35000000 INFO @ Tue, 02 Aug 2022 18:06:21: 37000000 INFO @ Tue, 02 Aug 2022 18:06:21: 36000000 INFO @ Tue, 02 Aug 2022 18:06:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.05_peaks.xls INFO @ Tue, 02 Aug 2022 18:06:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:06:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.05_summits.bed INFO @ Tue, 02 Aug 2022 18:06:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3306 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:06:30: 37000000 INFO @ Tue, 02 Aug 2022 18:06:30: 38000000 INFO @ Tue, 02 Aug 2022 18:06:38: 38000000 INFO @ Tue, 02 Aug 2022 18:06:39: 39000000 INFO @ Tue, 02 Aug 2022 18:06:42: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 18:06:42: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 18:06:42: #1 total tags in treatment: 19017291 INFO @ Tue, 02 Aug 2022 18:06:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:06:42: #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 18:06:43: #1 tags after filtering in treatment: 12774341 INFO @ Tue, 02 Aug 2022 18:06:43: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 18:06:43: #1 finished! INFO @ Tue, 02 Aug 2022 18:06:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:06:44: #2 number of paired peaks: 2932 INFO @ Tue, 02 Aug 2022 18:06:44: start model_add_line... INFO @ Tue, 02 Aug 2022 18:06:44: start X-correlation... INFO @ Tue, 02 Aug 2022 18:06:44: end of X-cor INFO @ Tue, 02 Aug 2022 18:06:44: #2 finished! INFO @ Tue, 02 Aug 2022 18:06:44: #2 predicted fragment length is 179 bps INFO @ Tue, 02 Aug 2022 18:06:44: #2 alternative fragment length(s) may be 0,15,179,295,328 bps INFO @ Tue, 02 Aug 2022 18:06:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.10_model.r WARNING @ Tue, 02 Aug 2022 18:06:44: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:06:44: #2 You may need to consider one of the other alternative d(s): 0,15,179,295,328 WARNING @ Tue, 02 Aug 2022 18:06:44: #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 18:06:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:06:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:06:46: 39000000 INFO @ Tue, 02 Aug 2022 18:06:49: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 18:06:49: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 18:06:49: #1 total tags in treatment: 19017291 INFO @ Tue, 02 Aug 2022 18:06:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 18:06:49: #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 18:06:49: #1 tags after filtering in treatment: 12774341 INFO @ Tue, 02 Aug 2022 18:06:49: #1 Redundant rate of treatment: 0.33 INFO @ Tue, 02 Aug 2022 18:06:49: #1 finished! INFO @ Tue, 02 Aug 2022 18:06:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 18:06:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 18:06:50: #2 number of paired peaks: 2932 INFO @ Tue, 02 Aug 2022 18:06:50: start model_add_line... INFO @ Tue, 02 Aug 2022 18:06:50: start X-correlation... INFO @ Tue, 02 Aug 2022 18:06:50: end of X-cor INFO @ Tue, 02 Aug 2022 18:06:50: #2 finished! INFO @ Tue, 02 Aug 2022 18:06:50: #2 predicted fragment length is 179 bps INFO @ Tue, 02 Aug 2022 18:06:50: #2 alternative fragment length(s) may be 0,15,179,295,328 bps INFO @ Tue, 02 Aug 2022 18:06:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.20_model.r WARNING @ Tue, 02 Aug 2022 18:06:50: #2 Since the d (179) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 18:06:50: #2 You may need to consider one of the other alternative d(s): 0,15,179,295,328 WARNING @ Tue, 02 Aug 2022 18:06:50: #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 18:06:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 18:06:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 18:07:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:07:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 18:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.10_peaks.xls INFO @ Tue, 02 Aug 2022 18:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.10_summits.bed INFO @ Tue, 02 Aug 2022 18:07:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1346 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 18:07:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.20_peaks.xls INFO @ Tue, 02 Aug 2022 18:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 18:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855765/SRX10855765.20_summits.bed INFO @ Tue, 02 Aug 2022 18:07:30: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (506 records, 4 fields): 25 millis CompletedMACS2peakCalling