Job ID = 14168320 SRX = ERX3978734 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25159807 spots for ERR3975743/ERR3975743.sra Written 25159807 spots for ERR3975743/ERR3975743.sra Read 19128986 spots for ERR3975749/ERR3975749.sra Written 19128986 spots for ERR3975749/ERR3975749.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169605 ("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: 01:11:25 44288793 reads; of these: 44288793 (100.00%) were paired; of these: 16931745 (38.23%) aligned concordantly 0 times 7909286 (17.86%) aligned concordantly exactly 1 time 19447762 (43.91%) aligned concordantly >1 times ---- 16931745 pairs aligned concordantly 0 times; of these: 2381715 (14.07%) aligned discordantly 1 time ---- 14550030 pairs aligned 0 times concordantly or discordantly; of these: 29100060 mates make up the pairs; of these: 14760598 (50.72%) aligned 0 times 647983 (2.23%) aligned exactly 1 time 13691479 (47.05%) aligned >1 times 83.34% overall alignment rate Time searching: 01:11:25 Overall time: 01:11:25 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 52 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] 17384173 / 29448351 = 0.5903 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 18:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.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 18:57:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:57:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:57:38: 1000000 INFO @ Fri, 10 Dec 2021 18:57:47: 2000000 INFO @ Fri, 10 Dec 2021 18:57:56: 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 18:57:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.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 18:57:58: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:57:58: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:58:06: 4000000 INFO @ Fri, 10 Dec 2021 18:58:07: 1000000 INFO @ Fri, 10 Dec 2021 18:58:16: 2000000 INFO @ Fri, 10 Dec 2021 18:58:16: 5000000 INFO @ Fri, 10 Dec 2021 18:58:24: 3000000 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 18:58:27: 6000000 INFO @ Fri, 10 Dec 2021 18:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.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 18:58:28: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:58:28: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:58:33: 4000000 INFO @ Fri, 10 Dec 2021 18:58:37: 7000000 INFO @ Fri, 10 Dec 2021 18:58:38: 1000000 INFO @ Fri, 10 Dec 2021 18:58:42: 5000000 INFO @ Fri, 10 Dec 2021 18:58:47: 8000000 INFO @ Fri, 10 Dec 2021 18:58:47: 2000000 INFO @ Fri, 10 Dec 2021 18:58:50: 6000000 INFO @ Fri, 10 Dec 2021 18:58:57: 3000000 INFO @ Fri, 10 Dec 2021 18:58:58: 9000000 INFO @ Fri, 10 Dec 2021 18:58:59: 7000000 INFO @ Fri, 10 Dec 2021 18:59:07: 4000000 INFO @ Fri, 10 Dec 2021 18:59:08: 10000000 INFO @ Fri, 10 Dec 2021 18:59:08: 8000000 INFO @ Fri, 10 Dec 2021 18:59:17: 9000000 INFO @ Fri, 10 Dec 2021 18:59:17: 5000000 INFO @ Fri, 10 Dec 2021 18:59:18: 11000000 INFO @ Fri, 10 Dec 2021 18:59:25: 10000000 INFO @ Fri, 10 Dec 2021 18:59:27: 6000000 INFO @ Fri, 10 Dec 2021 18:59:28: 12000000 INFO @ Fri, 10 Dec 2021 18:59:34: 11000000 INFO @ Fri, 10 Dec 2021 18:59:37: 7000000 INFO @ Fri, 10 Dec 2021 18:59:38: 13000000 INFO @ Fri, 10 Dec 2021 18:59:43: 12000000 INFO @ Fri, 10 Dec 2021 18:59:48: 8000000 INFO @ Fri, 10 Dec 2021 18:59:49: 14000000 INFO @ Fri, 10 Dec 2021 18:59:51: 13000000 INFO @ Fri, 10 Dec 2021 18:59:58: 9000000 INFO @ Fri, 10 Dec 2021 18:59:59: 15000000 INFO @ Fri, 10 Dec 2021 19:00:00: 14000000 INFO @ Fri, 10 Dec 2021 19:00:08: 10000000 INFO @ Fri, 10 Dec 2021 19:00:08: 15000000 INFO @ Fri, 10 Dec 2021 19:00:09: 16000000 INFO @ Fri, 10 Dec 2021 19:00:17: 16000000 INFO @ Fri, 10 Dec 2021 19:00:18: 11000000 INFO @ Fri, 10 Dec 2021 19:00:19: 17000000 INFO @ Fri, 10 Dec 2021 19:00:26: 17000000 INFO @ Fri, 10 Dec 2021 19:00:28: 12000000 INFO @ Fri, 10 Dec 2021 19:00:29: 18000000 INFO @ Fri, 10 Dec 2021 19:00:34: 18000000 INFO @ Fri, 10 Dec 2021 19:00:38: 13000000 INFO @ Fri, 10 Dec 2021 19:00:39: 19000000 INFO @ Fri, 10 Dec 2021 19:00:42: 19000000 INFO @ Fri, 10 Dec 2021 19:00:48: 14000000 INFO @ Fri, 10 Dec 2021 19:00:49: 20000000 INFO @ Fri, 10 Dec 2021 19:00:51: 20000000 INFO @ Fri, 10 Dec 2021 19:00:58: 15000000 INFO @ Fri, 10 Dec 2021 19:00:59: 21000000 INFO @ Fri, 10 Dec 2021 19:01:00: 21000000 INFO @ Fri, 10 Dec 2021 19:01:08: 16000000 INFO @ Fri, 10 Dec 2021 19:01:09: 22000000 INFO @ Fri, 10 Dec 2021 19:01:10: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:01:19: 17000000 INFO @ Fri, 10 Dec 2021 19:01:19: 23000000 INFO @ Fri, 10 Dec 2021 19:01:20: 23000000 INFO @ Fri, 10 Dec 2021 19:01:28: 18000000 INFO @ Fri, 10 Dec 2021 19:01:29: 24000000 INFO @ Fri, 10 Dec 2021 19:01:31: 24000000 INFO @ Fri, 10 Dec 2021 19:01:38: 19000000 INFO @ Fri, 10 Dec 2021 19:01:40: 25000000 INFO @ Fri, 10 Dec 2021 19:01:41: 25000000 INFO @ Fri, 10 Dec 2021 19:01:48: 20000000 INFO @ Fri, 10 Dec 2021 19:01:50: 26000000 INFO @ Fri, 10 Dec 2021 19:01:51: 26000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:01:58: 21000000 INFO @ Fri, 10 Dec 2021 19:02:00: 27000000 INFO @ Fri, 10 Dec 2021 19:02:01: 27000000 INFO @ Fri, 10 Dec 2021 19:02:08: 22000000 INFO @ Fri, 10 Dec 2021 19:02:11: 28000000 INFO @ Fri, 10 Dec 2021 19:02:12: 28000000 INFO @ Fri, 10 Dec 2021 19:02:18: 23000000 INFO @ Fri, 10 Dec 2021 19:02:21: 29000000 INFO @ Fri, 10 Dec 2021 19:02:22: 29000000 INFO @ Fri, 10 Dec 2021 19:02:27: 24000000 INFO @ Fri, 10 Dec 2021 19:02:32: 30000000 INFO @ Fri, 10 Dec 2021 19:02:33: 30000000 INFO @ Fri, 10 Dec 2021 19:02:37: 25000000 INFO @ Fri, 10 Dec 2021 19:02:42: 31000000 INFO @ Fri, 10 Dec 2021 19:02:43: 31000000 INFO @ Fri, 10 Dec 2021 19:02:47: 26000000 INFO @ Fri, 10 Dec 2021 19:02:52: 32000000 INFO @ Fri, 10 Dec 2021 19:02:53: 32000000 INFO @ Fri, 10 Dec 2021 19:02:57: 27000000 INFO @ Fri, 10 Dec 2021 19:03:02: 33000000 INFO @ Fri, 10 Dec 2021 19:03:03: 33000000 INFO @ Fri, 10 Dec 2021 19:03:07: 28000000 INFO @ Fri, 10 Dec 2021 19:03:12: 34000000 INFO @ Fri, 10 Dec 2021 19:03:14: 34000000 INFO @ Fri, 10 Dec 2021 19:03:17: 29000000 INFO @ Fri, 10 Dec 2021 19:03:23: 35000000 INFO @ Fri, 10 Dec 2021 19:03:24: 35000000 INFO @ Fri, 10 Dec 2021 19:03:26: 30000000 INFO @ Fri, 10 Dec 2021 19:03:33: 36000000 INFO @ Fri, 10 Dec 2021 19:03:34: 36000000 INFO @ Fri, 10 Dec 2021 19:03:36: 31000000 INFO @ Fri, 10 Dec 2021 19:03:44: 37000000 INFO @ Fri, 10 Dec 2021 19:03:45: 37000000 INFO @ Fri, 10 Dec 2021 19:03:46: 32000000 INFO @ Fri, 10 Dec 2021 19:03:54: 38000000 INFO @ Fri, 10 Dec 2021 19:03:55: 38000000 INFO @ Fri, 10 Dec 2021 19:03:55: 33000000 INFO @ Fri, 10 Dec 2021 19:04:05: 34000000 INFO @ Fri, 10 Dec 2021 19:04:05: 39000000 INFO @ Fri, 10 Dec 2021 19:04:05: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:04:05: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:04:05: #1 total tags in treatment: 10231443 INFO @ Fri, 10 Dec 2021 19:04:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:04:05: #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 19:04:06: #1 tags after filtering in treatment: 7239836 INFO @ Fri, 10 Dec 2021 19:04:06: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:04:06: #1 finished! INFO @ Fri, 10 Dec 2021 19:04:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:04:06: 39000000 INFO @ Fri, 10 Dec 2021 19:04:06: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:04:06: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:04:06: #1 total tags in treatment: 10231443 INFO @ Fri, 10 Dec 2021 19:04:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:04:06: #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 19:04:06: #2 number of paired peaks: 2378 INFO @ Fri, 10 Dec 2021 19:04:06: start model_add_line... INFO @ Fri, 10 Dec 2021 19:04:06: #1 tags after filtering in treatment: 7239836 INFO @ Fri, 10 Dec 2021 19:04:06: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:04:06: #1 finished! INFO @ Fri, 10 Dec 2021 19:04:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:04:06: start X-correlation... INFO @ Fri, 10 Dec 2021 19:04:06: end of X-cor INFO @ Fri, 10 Dec 2021 19:04:06: #2 finished! INFO @ Fri, 10 Dec 2021 19:04:06: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 19:04:06: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 19:04:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.05_model.r WARNING @ Fri, 10 Dec 2021 19:04:06: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:04:06: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 19:04:06: #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 19:04:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:04:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:04:07: #2 number of paired peaks: 2378 INFO @ Fri, 10 Dec 2021 19:04:07: start model_add_line... INFO @ Fri, 10 Dec 2021 19:04:07: start X-correlation... INFO @ Fri, 10 Dec 2021 19:04:07: end of X-cor INFO @ Fri, 10 Dec 2021 19:04:07: #2 finished! INFO @ Fri, 10 Dec 2021 19:04:07: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 19:04:07: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 19:04:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.10_model.r WARNING @ Fri, 10 Dec 2021 19:04:07: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:04:07: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 19:04:07: #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 19:04:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:04:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:04:14: 35000000 INFO @ Fri, 10 Dec 2021 19:04:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:04:23: 36000000 INFO @ Fri, 10 Dec 2021 19:04:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.05_summits.bed INFO @ Fri, 10 Dec 2021 19:04:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7990 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.10_summits.bed INFO @ Fri, 10 Dec 2021 19:04:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4412 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:04:32: 37000000 INFO @ Fri, 10 Dec 2021 19:04:41: 38000000 INFO @ Fri, 10 Dec 2021 19:04:50: 39000000 INFO @ Fri, 10 Dec 2021 19:04:50: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:04:50: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:04:50: #1 total tags in treatment: 10231443 INFO @ Fri, 10 Dec 2021 19:04:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:04:50: #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 19:04:51: #1 tags after filtering in treatment: 7239836 INFO @ Fri, 10 Dec 2021 19:04:51: #1 Redundant rate of treatment: 0.29 INFO @ Fri, 10 Dec 2021 19:04:51: #1 finished! INFO @ Fri, 10 Dec 2021 19:04:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:04:51: #2 number of paired peaks: 2378 INFO @ Fri, 10 Dec 2021 19:04:51: start model_add_line... INFO @ Fri, 10 Dec 2021 19:04:51: start X-correlation... INFO @ Fri, 10 Dec 2021 19:04:51: end of X-cor INFO @ Fri, 10 Dec 2021 19:04:51: #2 finished! INFO @ Fri, 10 Dec 2021 19:04:51: #2 predicted fragment length is 186 bps INFO @ Fri, 10 Dec 2021 19:04:51: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 10 Dec 2021 19:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.20_model.r WARNING @ Fri, 10 Dec 2021 19:04:51: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:04:51: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 10 Dec 2021 19:04:51: #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 19:04:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:05:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978734/ERX3978734.20_summits.bed INFO @ Fri, 10 Dec 2021 19:05:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1437 records, 4 fields): 3 millis CompletedMACS2peakCalling