Job ID = 14159541 SRX = SRX8845641 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 38664348 spots for SRR12345948/SRR12345948.sra Written 38664348 spots for SRR12345948/SRR12345948.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159858 ("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: 00:25:09 38664348 reads; of these: 38664348 (100.00%) were paired; of these: 3808731 (9.85%) aligned concordantly 0 times 28805092 (74.50%) aligned concordantly exactly 1 time 6050525 (15.65%) aligned concordantly >1 times ---- 3808731 pairs aligned concordantly 0 times; of these: 758462 (19.91%) aligned discordantly 1 time ---- 3050269 pairs aligned 0 times concordantly or discordantly; of these: 6100538 mates make up the pairs; of these: 5436770 (89.12%) aligned 0 times 310193 (5.08%) aligned exactly 1 time 353575 (5.80%) aligned >1 times 92.97% overall alignment rate Time searching: 00:25:10 Overall time: 00:25:10 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] 23439096 / 35494726 = 0.6604 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 23:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.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 23:00:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:00:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:00:50: 1000000 INFO @ Wed, 08 Dec 2021 23:00:55: 2000000 INFO @ Wed, 08 Dec 2021 23:00:59: 3000000 INFO @ Wed, 08 Dec 2021 23:01:04: 4000000 INFO @ Wed, 08 Dec 2021 23:01:08: 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 23:01:13: 6000000 INFO @ Wed, 08 Dec 2021 23:01:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.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 23:01:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:01:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:01:18: 7000000 INFO @ Wed, 08 Dec 2021 23:01:20: 1000000 INFO @ Wed, 08 Dec 2021 23:01:23: 8000000 INFO @ Wed, 08 Dec 2021 23:01:26: 2000000 INFO @ Wed, 08 Dec 2021 23:01:28: 9000000 INFO @ Wed, 08 Dec 2021 23:01:32: 3000000 INFO @ Wed, 08 Dec 2021 23:01:33: 10000000 INFO @ Wed, 08 Dec 2021 23:01:38: 4000000 INFO @ Wed, 08 Dec 2021 23:01:38: 11000000 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 23:01:43: 12000000 INFO @ Wed, 08 Dec 2021 23:01:44: 5000000 INFO @ Wed, 08 Dec 2021 23:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.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 23:01:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:01:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:01:49: 13000000 INFO @ Wed, 08 Dec 2021 23:01:50: 6000000 INFO @ Wed, 08 Dec 2021 23:01:50: 1000000 INFO @ Wed, 08 Dec 2021 23:01:54: 14000000 INFO @ Wed, 08 Dec 2021 23:01:55: 2000000 INFO @ Wed, 08 Dec 2021 23:01:56: 7000000 INFO @ Wed, 08 Dec 2021 23:01:59: 15000000 INFO @ Wed, 08 Dec 2021 23:02:01: 3000000 INFO @ Wed, 08 Dec 2021 23:02:02: 8000000 INFO @ Wed, 08 Dec 2021 23:02:05: 16000000 INFO @ Wed, 08 Dec 2021 23:02:06: 4000000 INFO @ Wed, 08 Dec 2021 23:02:08: 9000000 INFO @ Wed, 08 Dec 2021 23:02:10: 17000000 INFO @ Wed, 08 Dec 2021 23:02:11: 5000000 INFO @ Wed, 08 Dec 2021 23:02:14: 10000000 INFO @ Wed, 08 Dec 2021 23:02:16: 18000000 INFO @ Wed, 08 Dec 2021 23:02:17: 6000000 INFO @ Wed, 08 Dec 2021 23:02:20: 11000000 INFO @ Wed, 08 Dec 2021 23:02:21: 19000000 INFO @ Wed, 08 Dec 2021 23:02:22: 7000000 INFO @ Wed, 08 Dec 2021 23:02:26: 12000000 INFO @ Wed, 08 Dec 2021 23:02:26: 20000000 INFO @ Wed, 08 Dec 2021 23:02:27: 8000000 INFO @ Wed, 08 Dec 2021 23:02:31: 21000000 INFO @ Wed, 08 Dec 2021 23:02:32: 13000000 INFO @ Wed, 08 Dec 2021 23:02:32: 9000000 INFO @ Wed, 08 Dec 2021 23:02:36: 22000000 INFO @ Wed, 08 Dec 2021 23:02:37: 10000000 INFO @ Wed, 08 Dec 2021 23:02:38: 14000000 INFO @ Wed, 08 Dec 2021 23:02:41: 23000000 INFO @ Wed, 08 Dec 2021 23:02:42: 11000000 INFO @ Wed, 08 Dec 2021 23:02:43: 15000000 INFO @ Wed, 08 Dec 2021 23:02:47: 24000000 INFO @ Wed, 08 Dec 2021 23:02:48: 12000000 INFO @ Wed, 08 Dec 2021 23:02:50: 16000000 INFO @ Wed, 08 Dec 2021 23:02:52: 25000000 INFO @ Wed, 08 Dec 2021 23:02:52: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 23:02:52: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 23:02:52: #1 total tags in treatment: 11670936 INFO @ Wed, 08 Dec 2021 23:02:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:02:52: #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 23:02:52: #1 tags after filtering in treatment: 7305987 INFO @ Wed, 08 Dec 2021 23:02:52: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 08 Dec 2021 23:02:52: #1 finished! INFO @ Wed, 08 Dec 2021 23:02:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:02:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:02:53: #2 number of paired peaks: 1823 INFO @ Wed, 08 Dec 2021 23:02:53: start model_add_line... INFO @ Wed, 08 Dec 2021 23:02:53: start X-correlation... INFO @ Wed, 08 Dec 2021 23:02:53: end of X-cor INFO @ Wed, 08 Dec 2021 23:02:53: #2 finished! INFO @ Wed, 08 Dec 2021 23:02:53: #2 predicted fragment length is 88 bps INFO @ Wed, 08 Dec 2021 23:02:53: #2 alternative fragment length(s) may be 88 bps INFO @ Wed, 08 Dec 2021 23:02:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.05_model.r WARNING @ Wed, 08 Dec 2021 23:02:53: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:02:53: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Wed, 08 Dec 2021 23:02:53: #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 23:02:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:02:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:02:53: 13000000 INFO @ Wed, 08 Dec 2021 23:02:56: 17000000 INFO @ Wed, 08 Dec 2021 23:02:58: 14000000 INFO @ Wed, 08 Dec 2021 23:03:02: 18000000 INFO @ Wed, 08 Dec 2021 23:03:03: 15000000 INFO @ Wed, 08 Dec 2021 23:03:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:03:07: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:03:08: 16000000 INFO @ Wed, 08 Dec 2021 23:03:13: 17000000 INFO @ Wed, 08 Dec 2021 23:03:13: 20000000 INFO @ Wed, 08 Dec 2021 23:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.05_summits.bed INFO @ Wed, 08 Dec 2021 23:03:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (9935 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:03:18: 18000000 INFO @ Wed, 08 Dec 2021 23:03:19: 21000000 INFO @ Wed, 08 Dec 2021 23:03:24: 19000000 INFO @ Wed, 08 Dec 2021 23:03:25: 22000000 INFO @ Wed, 08 Dec 2021 23:03:29: 20000000 INFO @ Wed, 08 Dec 2021 23:03:31: 23000000 INFO @ Wed, 08 Dec 2021 23:03:34: 21000000 INFO @ Wed, 08 Dec 2021 23:03:36: 24000000 INFO @ Wed, 08 Dec 2021 23:03:39: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:03:42: 25000000 INFO @ Wed, 08 Dec 2021 23:03:42: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 23:03:42: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 23:03:42: #1 total tags in treatment: 11670936 INFO @ Wed, 08 Dec 2021 23:03:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:03:42: #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 23:03:42: #1 tags after filtering in treatment: 7305987 INFO @ Wed, 08 Dec 2021 23:03:42: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 08 Dec 2021 23:03:42: #1 finished! INFO @ Wed, 08 Dec 2021 23:03:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:03:43: #2 number of paired peaks: 1823 INFO @ Wed, 08 Dec 2021 23:03:43: start model_add_line... INFO @ Wed, 08 Dec 2021 23:03:43: start X-correlation... INFO @ Wed, 08 Dec 2021 23:03:43: end of X-cor INFO @ Wed, 08 Dec 2021 23:03:43: #2 finished! INFO @ Wed, 08 Dec 2021 23:03:43: #2 predicted fragment length is 88 bps INFO @ Wed, 08 Dec 2021 23:03:43: #2 alternative fragment length(s) may be 88 bps INFO @ Wed, 08 Dec 2021 23:03:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.10_model.r WARNING @ Wed, 08 Dec 2021 23:03:43: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:03:43: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Wed, 08 Dec 2021 23:03:43: #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 23:03:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:03:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:03:44: 23000000 INFO @ Wed, 08 Dec 2021 23:03:49: 24000000 INFO @ Wed, 08 Dec 2021 23:03:53: 25000000 INFO @ Wed, 08 Dec 2021 23:03:53: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 23:03:53: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 23:03:53: #1 total tags in treatment: 11670936 INFO @ Wed, 08 Dec 2021 23:03:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:03:53: #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 23:03:54: #1 tags after filtering in treatment: 7305987 INFO @ Wed, 08 Dec 2021 23:03:54: #1 Redundant rate of treatment: 0.37 INFO @ Wed, 08 Dec 2021 23:03:54: #1 finished! INFO @ Wed, 08 Dec 2021 23:03:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:03:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:03:54: #2 number of paired peaks: 1823 INFO @ Wed, 08 Dec 2021 23:03:54: start model_add_line... INFO @ Wed, 08 Dec 2021 23:03:54: start X-correlation... INFO @ Wed, 08 Dec 2021 23:03:54: end of X-cor INFO @ Wed, 08 Dec 2021 23:03:54: #2 finished! INFO @ Wed, 08 Dec 2021 23:03:54: #2 predicted fragment length is 88 bps INFO @ Wed, 08 Dec 2021 23:03:54: #2 alternative fragment length(s) may be 88 bps INFO @ Wed, 08 Dec 2021 23:03:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.20_model.r WARNING @ Wed, 08 Dec 2021 23:03:54: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:03:54: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Wed, 08 Dec 2021 23:03:54: #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 23:03:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:03:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:03:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.10_summits.bed INFO @ Wed, 08 Dec 2021 23:04:06: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6532 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:04:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:04:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:04:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:04:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845641/SRX8845641.20_summits.bed INFO @ Wed, 08 Dec 2021 23:04:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3597 records, 4 fields): 5 millis CompletedMACS2peakCalling