Job ID = 14159540 SRX = SRX8845640 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 39938522 spots for SRR12345947/SRR12345947.sra Written 39938522 spots for SRR12345947/SRR12345947.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159934 ("srTce11") 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: 00:29:38 39938522 reads; of these: 39938522 (100.00%) were paired; of these: 4519582 (11.32%) aligned concordantly 0 times 29561227 (74.02%) aligned concordantly exactly 1 time 5857713 (14.67%) aligned concordantly >1 times ---- 4519582 pairs aligned concordantly 0 times; of these: 755781 (16.72%) aligned discordantly 1 time ---- 3763801 pairs aligned 0 times concordantly or discordantly; of these: 7527602 mates make up the pairs; of these: 6806744 (90.42%) aligned 0 times 370763 (4.93%) aligned exactly 1 time 350095 (4.65%) aligned >1 times 91.48% overall alignment rate Time searching: 00:29:38 Overall time: 00:29:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 32 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 21427293 / 36056481 = 0.5943 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 @ Wed, 08 Dec 2021 23:05:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 23:05:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:05:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:05:32: 1000000 INFO @ Wed, 08 Dec 2021 23:05:37: 2000000 INFO @ Wed, 08 Dec 2021 23:05:42: 3000000 INFO @ Wed, 08 Dec 2021 23:05:47: 4000000 INFO @ Wed, 08 Dec 2021 23:05:52: 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 @ Wed, 08 Dec 2021 23:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 23:05:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:05:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:05:58: 6000000 INFO @ Wed, 08 Dec 2021 23:06:02: 1000000 INFO @ Wed, 08 Dec 2021 23:06:03: 7000000 INFO @ Wed, 08 Dec 2021 23:06:08: 2000000 INFO @ Wed, 08 Dec 2021 23:06:09: 8000000 INFO @ Wed, 08 Dec 2021 23:06:13: 3000000 INFO @ Wed, 08 Dec 2021 23:06:14: 9000000 INFO @ Wed, 08 Dec 2021 23:06:19: 4000000 INFO @ Wed, 08 Dec 2021 23:06:20: 10000000 INFO @ Wed, 08 Dec 2021 23:06:24: 5000000 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 @ Wed, 08 Dec 2021 23:06:26: 11000000 INFO @ Wed, 08 Dec 2021 23:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 23:06:26: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:06:26: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:06:30: 6000000 INFO @ Wed, 08 Dec 2021 23:06:32: 12000000 INFO @ Wed, 08 Dec 2021 23:06:33: 1000000 INFO @ Wed, 08 Dec 2021 23:06:37: 7000000 INFO @ Wed, 08 Dec 2021 23:06:38: 13000000 INFO @ Wed, 08 Dec 2021 23:06:41: 2000000 INFO @ Wed, 08 Dec 2021 23:06:43: 8000000 INFO @ Wed, 08 Dec 2021 23:06:44: 14000000 INFO @ Wed, 08 Dec 2021 23:06:48: 3000000 INFO @ Wed, 08 Dec 2021 23:06:49: 9000000 INFO @ Wed, 08 Dec 2021 23:06:51: 15000000 INFO @ Wed, 08 Dec 2021 23:06:55: 4000000 INFO @ Wed, 08 Dec 2021 23:06:55: 10000000 INFO @ Wed, 08 Dec 2021 23:06:57: 16000000 INFO @ Wed, 08 Dec 2021 23:07:02: 5000000 INFO @ Wed, 08 Dec 2021 23:07:02: 11000000 INFO @ Wed, 08 Dec 2021 23:07:03: 17000000 INFO @ Wed, 08 Dec 2021 23:07:08: 12000000 INFO @ Wed, 08 Dec 2021 23:07:09: 6000000 INFO @ Wed, 08 Dec 2021 23:07:09: 18000000 INFO @ Wed, 08 Dec 2021 23:07:14: 13000000 INFO @ Wed, 08 Dec 2021 23:07:16: 19000000 INFO @ Wed, 08 Dec 2021 23:07:16: 7000000 INFO @ Wed, 08 Dec 2021 23:07:21: 14000000 INFO @ Wed, 08 Dec 2021 23:07:22: 20000000 INFO @ Wed, 08 Dec 2021 23:07:23: 8000000 INFO @ Wed, 08 Dec 2021 23:07:27: 15000000 INFO @ Wed, 08 Dec 2021 23:07:28: 21000000 INFO @ Wed, 08 Dec 2021 23:07:30: 9000000 INFO @ Wed, 08 Dec 2021 23:07:33: 16000000 INFO @ Wed, 08 Dec 2021 23:07:34: 22000000 INFO @ Wed, 08 Dec 2021 23:07:37: 10000000 INFO @ Wed, 08 Dec 2021 23:07:39: 17000000 INFO @ Wed, 08 Dec 2021 23:07:41: 23000000 INFO @ Wed, 08 Dec 2021 23:07:44: 11000000 INFO @ Wed, 08 Dec 2021 23:07:46: 18000000 INFO @ Wed, 08 Dec 2021 23:07:47: 24000000 INFO @ Wed, 08 Dec 2021 23:07:51: 12000000 INFO @ Wed, 08 Dec 2021 23:07:52: 19000000 INFO @ Wed, 08 Dec 2021 23:07:54: 25000000 INFO @ Wed, 08 Dec 2021 23:07:58: 13000000 INFO @ Wed, 08 Dec 2021 23:07:58: 20000000 INFO @ Wed, 08 Dec 2021 23:08:00: 26000000 INFO @ Wed, 08 Dec 2021 23:08:05: 21000000 INFO @ Wed, 08 Dec 2021 23:08:05: 14000000 INFO @ Wed, 08 Dec 2021 23:08:06: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:08:11: 22000000 INFO @ Wed, 08 Dec 2021 23:08:12: 15000000 INFO @ Wed, 08 Dec 2021 23:08:12: 28000000 INFO @ Wed, 08 Dec 2021 23:08:17: 23000000 INFO @ Wed, 08 Dec 2021 23:08:19: 29000000 INFO @ Wed, 08 Dec 2021 23:08:19: 16000000 INFO @ Wed, 08 Dec 2021 23:08:24: 24000000 INFO @ Wed, 08 Dec 2021 23:08:25: 30000000 INFO @ Wed, 08 Dec 2021 23:08:26: 17000000 INFO @ Wed, 08 Dec 2021 23:08:26: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 23:08:26: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 23:08:26: #1 total tags in treatment: 14204565 INFO @ Wed, 08 Dec 2021 23:08:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:08:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:08:27: #1 tags after filtering in treatment: 9214621 INFO @ Wed, 08 Dec 2021 23:08:27: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 08 Dec 2021 23:08:27: #1 finished! INFO @ Wed, 08 Dec 2021 23:08:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:08:27: #2 number of paired peaks: 1127 INFO @ Wed, 08 Dec 2021 23:08:27: start model_add_line... INFO @ Wed, 08 Dec 2021 23:08:27: start X-correlation... INFO @ Wed, 08 Dec 2021 23:08:27: end of X-cor INFO @ Wed, 08 Dec 2021 23:08:27: #2 finished! INFO @ Wed, 08 Dec 2021 23:08:27: #2 predicted fragment length is 84 bps INFO @ Wed, 08 Dec 2021 23:08:27: #2 alternative fragment length(s) may be 84 bps INFO @ Wed, 08 Dec 2021 23:08:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.05_model.r WARNING @ Wed, 08 Dec 2021 23:08:27: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:08:27: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Wed, 08 Dec 2021 23:08:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:08:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:08:30: 25000000 INFO @ Wed, 08 Dec 2021 23:08:33: 18000000 INFO @ Wed, 08 Dec 2021 23:08:36: 26000000 INFO @ Wed, 08 Dec 2021 23:08:40: 19000000 INFO @ Wed, 08 Dec 2021 23:08:42: 27000000 INFO @ Wed, 08 Dec 2021 23:08:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:08:47: 20000000 INFO @ Wed, 08 Dec 2021 23:08:49: 28000000 INFO @ Wed, 08 Dec 2021 23:08:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:08:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:08:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.05_summits.bed INFO @ Wed, 08 Dec 2021 23:08:54: Done! INFO @ Wed, 08 Dec 2021 23:08:54: 21000000 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9341 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:08:55: 29000000 INFO @ Wed, 08 Dec 2021 23:09:01: 30000000 INFO @ Wed, 08 Dec 2021 23:09:01: 22000000 INFO @ Wed, 08 Dec 2021 23:09:02: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 23:09:02: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 23:09:02: #1 total tags in treatment: 14204565 INFO @ Wed, 08 Dec 2021 23:09:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:09:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:09:03: #1 tags after filtering in treatment: 9214621 INFO @ Wed, 08 Dec 2021 23:09:03: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 08 Dec 2021 23:09:03: #1 finished! INFO @ Wed, 08 Dec 2021 23:09:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:09:03: #2 number of paired peaks: 1127 INFO @ Wed, 08 Dec 2021 23:09:03: start model_add_line... INFO @ Wed, 08 Dec 2021 23:09:04: start X-correlation... INFO @ Wed, 08 Dec 2021 23:09:04: end of X-cor INFO @ Wed, 08 Dec 2021 23:09:04: #2 finished! INFO @ Wed, 08 Dec 2021 23:09:04: #2 predicted fragment length is 84 bps INFO @ Wed, 08 Dec 2021 23:09:04: #2 alternative fragment length(s) may be 84 bps INFO @ Wed, 08 Dec 2021 23:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.10_model.r WARNING @ Wed, 08 Dec 2021 23:09:04: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:09:04: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Wed, 08 Dec 2021 23:09:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:09:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:09:08: 23000000 INFO @ Wed, 08 Dec 2021 23:09:15: 24000000 INFO @ Wed, 08 Dec 2021 23:09:21: 25000000 INFO @ Wed, 08 Dec 2021 23:09:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:09:27: 26000000 INFO @ Wed, 08 Dec 2021 23:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.10_summits.bed INFO @ Wed, 08 Dec 2021 23:09:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6131 records, 4 fields): 233 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:09:34: 27000000 INFO @ Wed, 08 Dec 2021 23:09:40: 28000000 INFO @ Wed, 08 Dec 2021 23:09:47: 29000000 INFO @ Wed, 08 Dec 2021 23:09:53: 30000000 INFO @ Wed, 08 Dec 2021 23:09:54: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 23:09:54: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 23:09:54: #1 total tags in treatment: 14204565 INFO @ Wed, 08 Dec 2021 23:09:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:09:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 23:09:55: #1 tags after filtering in treatment: 9214621 INFO @ Wed, 08 Dec 2021 23:09:55: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 08 Dec 2021 23:09:55: #1 finished! INFO @ Wed, 08 Dec 2021 23:09:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:09:55: #2 number of paired peaks: 1127 INFO @ Wed, 08 Dec 2021 23:09:55: start model_add_line... INFO @ Wed, 08 Dec 2021 23:09:55: start X-correlation... INFO @ Wed, 08 Dec 2021 23:09:55: end of X-cor INFO @ Wed, 08 Dec 2021 23:09:55: #2 finished! INFO @ Wed, 08 Dec 2021 23:09:55: #2 predicted fragment length is 84 bps INFO @ Wed, 08 Dec 2021 23:09:55: #2 alternative fragment length(s) may be 84 bps INFO @ Wed, 08 Dec 2021 23:09:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.20_model.r WARNING @ Wed, 08 Dec 2021 23:09:55: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:09:55: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Wed, 08 Dec 2021 23:09:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 23:09:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:10:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:10:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:10:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:10:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845640/SRX8845640.20_summits.bed INFO @ Wed, 08 Dec 2021 23:10:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (3062 records, 4 fields): 5 millis CompletedMACS2peakCalling