Job ID = 14171365 SRX = SRX9304584 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 49875696 spots for SRR12837081/SRR12837081.sra Written 49875696 spots for SRR12837081/SRR12837081.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172066 ("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: 00:49:03 49875696 reads; of these: 49875696 (100.00%) were paired; of these: 11871602 (23.80%) aligned concordantly 0 times 33019303 (66.20%) aligned concordantly exactly 1 time 4984791 (9.99%) aligned concordantly >1 times ---- 11871602 pairs aligned concordantly 0 times; of these: 419583 (3.53%) aligned discordantly 1 time ---- 11452019 pairs aligned 0 times concordantly or discordantly; of these: 22904038 mates make up the pairs; of these: 21845762 (95.38%) aligned 0 times 780016 (3.41%) aligned exactly 1 time 278260 (1.21%) aligned >1 times 78.10% overall alignment rate Time searching: 00:49:03 Overall time: 00:49:03 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] 20374097 / 25584770 = 0.7963 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 12:34:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.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 12:34:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:34:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:34:59: 1000000 INFO @ Sat, 11 Dec 2021 12:35:04: 2000000 INFO @ Sat, 11 Dec 2021 12:35:09: 3000000 INFO @ Sat, 11 Dec 2021 12:35:13: 4000000 INFO @ Sat, 11 Dec 2021 12:35:18: 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 12:35:23: 6000000 INFO @ Sat, 11 Dec 2021 12:35:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.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 12:35:24: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:35:24: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:35:29: 7000000 INFO @ Sat, 11 Dec 2021 12:35:30: 1000000 INFO @ Sat, 11 Dec 2021 12:35:36: 8000000 INFO @ Sat, 11 Dec 2021 12:35:37: 2000000 INFO @ Sat, 11 Dec 2021 12:35:42: 9000000 INFO @ Sat, 11 Dec 2021 12:35:44: 3000000 INFO @ Sat, 11 Dec 2021 12:35:48: 10000000 INFO @ Sat, 11 Dec 2021 12:35:51: 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 12:35:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.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 12:35:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:35:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:35:54: 11000000 INFO @ Sat, 11 Dec 2021 12:35:57: 5000000 INFO @ Sat, 11 Dec 2021 12:36:00: 1000000 INFO @ Sat, 11 Dec 2021 12:36:00: 12000000 INFO @ Sat, 11 Dec 2021 12:36:04: 6000000 INFO @ Sat, 11 Dec 2021 12:36:06: 2000000 INFO @ Sat, 11 Dec 2021 12:36:06: 13000000 INFO @ Sat, 11 Dec 2021 12:36:10: 7000000 INFO @ Sat, 11 Dec 2021 12:36:12: 3000000 INFO @ Sat, 11 Dec 2021 12:36:12: 14000000 INFO @ Sat, 11 Dec 2021 12:36:17: 8000000 INFO @ Sat, 11 Dec 2021 12:36:18: 4000000 INFO @ Sat, 11 Dec 2021 12:36:18: 15000000 INFO @ Sat, 11 Dec 2021 12:36:24: 9000000 INFO @ Sat, 11 Dec 2021 12:36:24: 5000000 INFO @ Sat, 11 Dec 2021 12:36:25: 16000000 INFO @ Sat, 11 Dec 2021 12:36:30: 6000000 INFO @ Sat, 11 Dec 2021 12:36:30: 10000000 INFO @ Sat, 11 Dec 2021 12:36:31: 17000000 INFO @ Sat, 11 Dec 2021 12:36:36: 7000000 INFO @ Sat, 11 Dec 2021 12:36:37: 18000000 INFO @ Sat, 11 Dec 2021 12:36:37: 11000000 INFO @ Sat, 11 Dec 2021 12:36:42: 8000000 INFO @ Sat, 11 Dec 2021 12:36:43: 19000000 INFO @ Sat, 11 Dec 2021 12:36:44: 12000000 INFO @ Sat, 11 Dec 2021 12:36:49: 9000000 INFO @ Sat, 11 Dec 2021 12:36:49: 20000000 INFO @ Sat, 11 Dec 2021 12:36:51: 13000000 INFO @ Sat, 11 Dec 2021 12:36:55: 10000000 INFO @ Sat, 11 Dec 2021 12:36:55: 21000000 INFO @ Sat, 11 Dec 2021 12:36:59: 14000000 INFO @ Sat, 11 Dec 2021 12:37:01: 11000000 INFO @ Sat, 11 Dec 2021 12:37:01: 22000000 INFO @ Sat, 11 Dec 2021 12:37:05: 15000000 INFO @ Sat, 11 Dec 2021 12:37:07: 12000000 INFO @ Sat, 11 Dec 2021 12:37:07: 23000000 INFO @ Sat, 11 Dec 2021 12:37:12: 16000000 INFO @ Sat, 11 Dec 2021 12:37:13: 24000000 INFO @ Sat, 11 Dec 2021 12:37:13: 13000000 INFO @ Sat, 11 Dec 2021 12:37:19: 17000000 INFO @ Sat, 11 Dec 2021 12:37:19: 25000000 INFO @ Sat, 11 Dec 2021 12:37:19: 14000000 INFO @ Sat, 11 Dec 2021 12:37:25: 15000000 INFO @ Sat, 11 Dec 2021 12:37:25: 26000000 INFO @ Sat, 11 Dec 2021 12:37:26: 18000000 INFO @ Sat, 11 Dec 2021 12:37:31: 16000000 INFO @ Sat, 11 Dec 2021 12:37:31: 27000000 INFO @ Sat, 11 Dec 2021 12:37:33: 19000000 INFO @ Sat, 11 Dec 2021 12:37:37: 17000000 INFO @ Sat, 11 Dec 2021 12:37:38: 28000000 INFO @ Sat, 11 Dec 2021 12:37:39: 20000000 INFO @ Sat, 11 Dec 2021 12:37:43: 18000000 INFO @ Sat, 11 Dec 2021 12:37:44: 29000000 INFO @ Sat, 11 Dec 2021 12:37:46: 21000000 INFO @ Sat, 11 Dec 2021 12:37:49: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:37:51: 30000000 INFO @ Sat, 11 Dec 2021 12:37:53: 22000000 INFO @ Sat, 11 Dec 2021 12:37:55: 20000000 INFO @ Sat, 11 Dec 2021 12:37:57: 31000000 INFO @ Sat, 11 Dec 2021 12:38:00: 23000000 INFO @ Sat, 11 Dec 2021 12:38:01: 21000000 INFO @ Sat, 11 Dec 2021 12:38:03: 32000000 INFO @ Sat, 11 Dec 2021 12:38:06: 24000000 INFO @ Sat, 11 Dec 2021 12:38:07: 22000000 INFO @ Sat, 11 Dec 2021 12:38:09: 33000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:38:13: 23000000 INFO @ Sat, 11 Dec 2021 12:38:13: 25000000 INFO @ Sat, 11 Dec 2021 12:38:15: 34000000 INFO @ Sat, 11 Dec 2021 12:38:19: 24000000 INFO @ Sat, 11 Dec 2021 12:38:20: 26000000 INFO @ Sat, 11 Dec 2021 12:38:21: 35000000 INFO @ Sat, 11 Dec 2021 12:38:25: 25000000 INFO @ Sat, 11 Dec 2021 12:38:27: 27000000 INFO @ Sat, 11 Dec 2021 12:38:27: 36000000 INFO @ Sat, 11 Dec 2021 12:38:31: 26000000 INFO @ Sat, 11 Dec 2021 12:38:33: 37000000 INFO @ Sat, 11 Dec 2021 12:38:34: 28000000 INFO @ Sat, 11 Dec 2021 12:38:35: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:38:35: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:38:35: #1 total tags in treatment: 17724143 INFO @ Sat, 11 Dec 2021 12:38:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:38:35: #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 12:38:35: #1 tags after filtering in treatment: 5521943 INFO @ Sat, 11 Dec 2021 12:38:35: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 11 Dec 2021 12:38:35: #1 finished! INFO @ Sat, 11 Dec 2021 12:38:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:38:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:38:35: #2 number of paired peaks: 4242 INFO @ Sat, 11 Dec 2021 12:38:35: start model_add_line... INFO @ Sat, 11 Dec 2021 12:38:35: start X-correlation... INFO @ Sat, 11 Dec 2021 12:38:35: end of X-cor INFO @ Sat, 11 Dec 2021 12:38:35: #2 finished! INFO @ Sat, 11 Dec 2021 12:38:35: #2 predicted fragment length is 78 bps INFO @ Sat, 11 Dec 2021 12:38:35: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 11 Dec 2021 12:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.05_model.r WARNING @ Sat, 11 Dec 2021 12:38:36: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:38:36: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 11 Dec 2021 12:38:36: #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 12:38:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:38:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:38:37: 27000000 INFO @ Sat, 11 Dec 2021 12:38:42: 29000000 INFO @ Sat, 11 Dec 2021 12:38:43: 28000000 INFO @ Sat, 11 Dec 2021 12:38:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:38:49: 30000000 INFO @ Sat, 11 Dec 2021 12:38:49: 29000000 INFO @ Sat, 11 Dec 2021 12:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.05_summits.bed INFO @ Sat, 11 Dec 2021 12:38:53: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15716 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:38:56: 30000000 INFO @ Sat, 11 Dec 2021 12:38:57: 31000000 INFO @ Sat, 11 Dec 2021 12:39:02: 31000000 INFO @ Sat, 11 Dec 2021 12:39:03: 32000000 INFO @ Sat, 11 Dec 2021 12:39:08: 32000000 INFO @ Sat, 11 Dec 2021 12:39:10: 33000000 INFO @ Sat, 11 Dec 2021 12:39:14: 33000000 INFO @ Sat, 11 Dec 2021 12:39:17: 34000000 INFO @ Sat, 11 Dec 2021 12:39:20: 34000000 INFO @ Sat, 11 Dec 2021 12:39:24: 35000000 INFO @ Sat, 11 Dec 2021 12:39:27: 35000000 INFO @ Sat, 11 Dec 2021 12:39:31: 36000000 INFO @ Sat, 11 Dec 2021 12:39:33: 36000000 INFO @ Sat, 11 Dec 2021 12:39:37: 37000000 INFO @ Sat, 11 Dec 2021 12:39:39: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:39:39: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:39:39: #1 total tags in treatment: 17724143 INFO @ Sat, 11 Dec 2021 12:39:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:39:39: #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 12:39:39: #1 tags after filtering in treatment: 5521943 INFO @ Sat, 11 Dec 2021 12:39:39: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 11 Dec 2021 12:39:39: #1 finished! INFO @ Sat, 11 Dec 2021 12:39:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:39:39: 37000000 INFO @ Sat, 11 Dec 2021 12:39:40: #2 number of paired peaks: 4242 INFO @ Sat, 11 Dec 2021 12:39:40: start model_add_line... INFO @ Sat, 11 Dec 2021 12:39:40: start X-correlation... INFO @ Sat, 11 Dec 2021 12:39:40: end of X-cor INFO @ Sat, 11 Dec 2021 12:39:40: #2 finished! INFO @ Sat, 11 Dec 2021 12:39:40: #2 predicted fragment length is 78 bps INFO @ Sat, 11 Dec 2021 12:39:40: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 11 Dec 2021 12:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.10_model.r WARNING @ Sat, 11 Dec 2021 12:39:40: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:39:40: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 11 Dec 2021 12:39:40: #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 12:39:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:39:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:39:40: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 12:39:40: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 12:39:40: #1 total tags in treatment: 17724143 INFO @ Sat, 11 Dec 2021 12:39:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:39:40: #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 12:39:41: #1 tags after filtering in treatment: 5521943 INFO @ Sat, 11 Dec 2021 12:39:41: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 11 Dec 2021 12:39:41: #1 finished! INFO @ Sat, 11 Dec 2021 12:39:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:39:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:39:41: #2 number of paired peaks: 4242 INFO @ Sat, 11 Dec 2021 12:39:41: start model_add_line... INFO @ Sat, 11 Dec 2021 12:39:41: start X-correlation... INFO @ Sat, 11 Dec 2021 12:39:41: end of X-cor INFO @ Sat, 11 Dec 2021 12:39:41: #2 finished! INFO @ Sat, 11 Dec 2021 12:39:41: #2 predicted fragment length is 78 bps INFO @ Sat, 11 Dec 2021 12:39:41: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 11 Dec 2021 12:39:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.20_model.r WARNING @ Sat, 11 Dec 2021 12:39:41: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:39:41: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 11 Dec 2021 12:39:41: #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 12:39:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:39:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:39:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:39:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:39:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:39:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:39:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.10_summits.bed INFO @ Sat, 11 Dec 2021 12:39:57: Done! pass1 - making usageList (14 chroms): 10 millis pass2 - checking and writing primary data (8139 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:39:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:39:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:39:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9304584/SRX9304584.20_summits.bed INFO @ Sat, 11 Dec 2021 12:39:59: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (2078 records, 4 fields): 3 millis CompletedMACS2peakCalling