[2024-01-25 18:45:05,571] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:45:05,572] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:45:05,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg34e1ba42-0125-4254-aeb0-6f44a63e9080/dqc_reference
[2024-01-25 18:45:06,829] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:45:06,830] [INFO] Task started: Prodigal
[2024-01-25 18:45:06,830] [INFO] Running command: gunzip -c /var/lib/cwl/stg586716cb-2bff-4c31-aeec-4c3db39a171a/GCF_003544935.1_ASM354493v1_genomic.fna.gz | prodigal -d GCF_003544935.1_ASM354493v1_genomic.fna/cds.fna -a GCF_003544935.1_ASM354493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:45:10,790] [INFO] Task succeeded: Prodigal
[2024-01-25 18:45:10,790] [INFO] Task started: HMMsearch
[2024-01-25 18:45:10,790] [INFO] Running command: hmmsearch --tblout GCF_003544935.1_ASM354493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34e1ba42-0125-4254-aeb0-6f44a63e9080/dqc_reference/reference_markers.hmm GCF_003544935.1_ASM354493v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:45:11,012] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:45:11,013] [INFO] Found 6/6 markers.
[2024-01-25 18:45:11,040] [INFO] Query marker FASTA was written to GCF_003544935.1_ASM354493v1_genomic.fna/markers.fasta
[2024-01-25 18:45:11,040] [INFO] Task started: Blastn
[2024-01-25 18:45:11,040] [INFO] Running command: blastn -query GCF_003544935.1_ASM354493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34e1ba42-0125-4254-aeb0-6f44a63e9080/dqc_reference/reference_markers.fasta -out GCF_003544935.1_ASM354493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:11,596] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:11,598] [INFO] Selected 8 target genomes.
[2024-01-25 18:45:11,599] [INFO] Target genome list was writen to GCF_003544935.1_ASM354493v1_genomic.fna/target_genomes.txt
[2024-01-25 18:45:11,604] [INFO] Task started: fastANI
[2024-01-25 18:45:11,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg586716cb-2bff-4c31-aeec-4c3db39a171a/GCF_003544935.1_ASM354493v1_genomic.fna.gz --refList GCF_003544935.1_ASM354493v1_genomic.fna/target_genomes.txt --output GCF_003544935.1_ASM354493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:17,077] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:17,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34e1ba42-0125-4254-aeb0-6f44a63e9080/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:17,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34e1ba42-0125-4254-aeb0-6f44a63e9080/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:17,084] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:45:17,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:45:17,084] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	100.0	929	933	95	conclusive
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	99.949	884	933	95	conclusive
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	82.2794	637	933	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	82.2717	586	933	95	below_threshold
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	82.2162	623	933	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	81.9141	617	933	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	81.8617	612	933	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	81.6815	582	933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:17,085] [INFO] DFAST Taxonomy check result was written to GCF_003544935.1_ASM354493v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:17,086] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:17,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:17,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34e1ba42-0125-4254-aeb0-6f44a63e9080/dqc_reference/checkm_data
[2024-01-25 18:45:17,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:17,117] [INFO] Task started: CheckM
[2024-01-25 18:45:17,117] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003544935.1_ASM354493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003544935.1_ASM354493v1_genomic.fna/checkm_input GCF_003544935.1_ASM354493v1_genomic.fna/checkm_result
[2024-01-25 18:45:34,700] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:34,702] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:34,722] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:34,722] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:34,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003544935.1_ASM354493v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:34,723] [INFO] Task started: Blastn
[2024-01-25 18:45:34,723] [INFO] Running command: blastn -query GCF_003544935.1_ASM354493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34e1ba42-0125-4254-aeb0-6f44a63e9080/dqc_reference/reference_markers_gtdb.fasta -out GCF_003544935.1_ASM354493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:35,537] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:35,540] [INFO] Selected 7 target genomes.
[2024-01-25 18:45:35,540] [INFO] Target genome list was writen to GCF_003544935.1_ASM354493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:35,559] [INFO] Task started: fastANI
[2024-01-25 18:45:35,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg586716cb-2bff-4c31-aeec-4c3db39a171a/GCF_003544935.1_ASM354493v1_genomic.fna.gz --refList GCF_003544935.1_ASM354493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003544935.1_ASM354493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:40,895] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:40,900] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:40,901] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003544935.1	s__Malaciobacter molluscorum	100.0	928	933	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	conclusive
GCA_004116725.1	s__Malaciobacter sp004116725	90.4372	762	933	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116495.1	s__Malaciobacter sp004116495	86.5353	718	933	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837275.1	s__Malaciobacter halophilus	82.2698	586	933	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003544855.1	s__Malaciobacter marinus	82.2317	643	933	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	98.03	95.41	0.91	0.86	14	-
GCF_003346775.1	s__Malaciobacter mytili	81.8334	614	933	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
GCA_001895145.1	s__Halarcobacter sp001895145	79.1293	411	933	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:40,903] [INFO] GTDB search result was written to GCF_003544935.1_ASM354493v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:40,903] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:40,906] [INFO] DFAST_QC result json was written to GCF_003544935.1_ASM354493v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:40,906] [INFO] DFAST_QC completed!
[2024-01-25 18:45:40,906] [INFO] Total running time: 0h0m35s