Genome Assembly:

1
2
3
4
5
6
7
8
[sivanandan.chudalayandi@ceres-dtn-1 mosquito]$ pwd
/90daydata/isu_gif_vrsc/Siva/mosquito
[sivanandan.chudalayandi@ceres-dtn-1 mosquito]$ more download.txt
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/085/SRR12121585/SRR12121585_subreads.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/086/SRR12121586/SRR12121586_subreads.fastq.gz
[sivanandan.chudalayandi@ceres-dtn-1 mosquito]$ more download.sh
parallel <download.txt
[sivanandan.chudalayandi@ceres-dtn-1 mosquito]$
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
1040  cd /project/isu_gif_vrsc/Siva/software/
 1041  git init
 1042  git clone https://github.com/chhylp123/hifiasm
 1043  ls
 1044  cd hifiasm/
 1045  make
 1046  ls
 1047  pwd
 1048  nano ~/.bashrc
 1049  nano ~/.bash_profile
 1050  nano ~/.bashrc
 1051  pwd
 1052  /project/isu_gif_vrsc/Siva/software/hifiasm/hifiasm
 1053  nano ~/.bashrc
 1054  source ~/.bashrc
 1055  hifiasm
 1056  history

1
2
3
[sivanandan.chudalayandi@ceres19-compute-35 mosquito]$ pwd
/project/isu_gif_vrsc/Siva/Service/mosquito
[sivanandan.chudalayandi@ceres19-compute-35 mosquito]$ hifiasm -o anopheles.asm -t20 SRR12121585_subreads.fastq.gz SRR12121586_subreads.fastq.gz >& anopheles.log&

Files produced:

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
anopheles.log
anopheles.asm.a_ctg.lowQ.bed
anopheles.asm.a_ctg.gfa
anopheles.asm.a_ctg.noseq.gfa
anopheles.asm.p_ctg.lowQ.bed
anopheles.asm.p_ctg.gfa
anopheles.asm.p_ctg.noseq.gfa
anopheles.asm.p_utg.lowQ.bed
anopheles.asm.p_utg.noseq.gfa
anopheles.asm.p_utg.gfa
anopheles.asm.r_utg.lowQ.bed
anopheles.asm.r_utg.gfa
anopheles.asm.r_utg.noseq.gfa
anopheles.asm.ovlp.reverse.bin
anopheles.asm.ovlp.source.bin
anopheles.asm.ec.bin

weirdly, I am unable to see anything in /project/isu_gif_vrsc/Siva/software/ though I had git cloned hifiasm there.

For Sylvie.Quiniou https://usda-scinet.atlassian.net/browse/VRSC-3020
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
6:05 AM; Sat Feb 20; 2021
# wonder why inputs are fasta?
# why using conda... when installation seems to be very simple
# test is working saw log files with kmer frequencies being written from 6:45 am

these are her conda commands and the batch job submision:

module load miniconda
source activate hifiasm
sbatch hifiasmdiploid.sh



[root@ceres19-compute-30 hifiasm_check]# pwd
/lustre/project/isu_gif_vrsc/Siva/Service/hifiasm_check
[root@ceres19-compute-30 hifiasm_check]# ls
hifiasm.man  SQ_hifiasm  test.log
[root@ceres19-compute-30 hifiasm_check]# ls -lth
total 4.0K
-rw-r--r--. 1 root proj-isu_gif_vrsc    0 Feb 20 06:05 test.log
-rw-r--r--. 1 root proj-isu_gif_vrsc 2.8K Feb 20 05:58 hifiasm.man
lrwxrwxrwx. 1 root proj-isu_gif_vrsc   39 Feb 20 05:16 SQ_hifiasm -> /project/tgbs_analysis/HIFIASM-CCSCCBL1
[root@ceres19-compute-30 hifiasm_check]#

# got kicked out of the job around 2 pm.