EMIRGE ERROR

[mariarovis...@gmail.com]

Good morning,

My name is Maria. I a trying to run EMIRGE however I haven't been very successful with that.

I came across with this error:

EMIRGE started at Fri May 11 13:39:06 2018

Performing initial mapping with command:

cat  /mnt/cb2a911f-2d7d-48b2-8f97-a30575585833/Resilience/N05114_MM_HZ1711011_metaDNASEQ/PF_data/clean1n/ready_m1_1.fq |  bowtie --phred33-quals -t -p 1 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128 --minins 291 --maxins 316 /mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE -1 - -2 /mnt/cb2a911f-2d7d-48b2-8f97-a30575585833/Resilience/N05114_MM_HZ1711011_metaDNASEQ/PF_data/clean1n/ready_m1_2.fq | samtools view -b -S -u -F 0x0004 - > /mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/DIR/initial_mapping/initial_bowtie_mapping.PE.bam 

Could not locate a Bowtie index corresponding to basename "/mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE"

Overall time: 00:00:00

Command: /usr/bin/bowtie-align-s --wrapper basic-0 --phred33-quals -t -p 1 -n 3 -l 20 -e 300 --best --sam --chunkmbs 128 --minins 291 --maxins 316 -1 - -2 /mnt/cb2a911f-2d7d-48b2-8f97-a30575585833/Resilience/N05114_MM_HZ1711011_metaDNASEQ/PF_data/clean1n/ready_m1_2.fq /mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE 

cat: write error: Broken pipe

Beginning initialization at Fri May 11 13:39:06 2018...

Reading bam file /mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/DIR/initial_mapping/initial_bowtie_mapping.PE.bam at Fri May 11 13:39:06 2018...

Traceback (most recent call last):

  File "/mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/emirge.py", line 1697, in <module>

    main()

  File "/mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/emirge.py", line 1681, in main

    em.initialize_EM(options.mapping, options.fasta_db)

  File "/mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/emirge.py", line 337, in initialize_EM

    self.read_bam(bam_filename, reference_fasta_filename)

  File "/mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/emirge.py", line 251, in read_bam

    bamfile = pysam.Samfile(bam_filename, "rb")

  File "pysam/libcalignmentfile.pyx", line 729, in pysam.libcalignmentfile.AlignmentFile.__cinit__

  File "pysam/libcalignmentfile.pyx", line 969, in pysam.libcalignmentfile.AlignmentFile._open

ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False

Could not locate a Bowtie index corresponding to basename "/mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE"

In my directory I have the following files:

SILVA_132_SSURef_Nr99_tax_silva_trunc.fasta.gz

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fasta

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.1.ebwt

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.2.ebwt

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.3.ebwt

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.4.ebwt

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta.fai

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.rev.1.ebwt

SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.rev.2.ebwt

Can anyone help me with that please?

Best regards

[もみもみお]

I think that you should do  like this 

-b /mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed
You must not do like this

-b /mnt/7c8fd4e1-c269-4a73-9454-b988d49f9139/EMIRGE/SILVA_132_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.*.ebwt

2018年5月12日土曜日 1:27:15 UTC+9 mariarovis...@gmail.com: