[2024-01-24 14:39:45,823] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg2880edc3-4219-4b12-860c-cb4e1380b86f/dqc_reference
[2024-01-24 14:39:48,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,366] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,366] [INFO] Running command: gunzip -c /var/lib/cwl/stgaac702f8-0f2f-4489-a41d-7664edac83f3/GCF_006228385.1_ASM622838v1_genomic.fna.gz | prodigal -d GCF_006228385.1_ASM622838v1_genomic.fna/cds.fna -a GCF_006228385.1_ASM622838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:58,880] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:58,880] [INFO] Task started: HMMsearch
[2024-01-24 14:39:58,880] [INFO] Running command: hmmsearch --tblout GCF_006228385.1_ASM622838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2880edc3-4219-4b12-860c-cb4e1380b86f/dqc_reference/reference_markers.hmm GCF_006228385.1_ASM622838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:59,367] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:59,368] [INFO] Found 6/6 markers.
[2024-01-24 14:39:59,409] [INFO] Query marker FASTA was written to GCF_006228385.1_ASM622838v1_genomic.fna/markers.fasta
[2024-01-24 14:39:59,410] [INFO] Task started: Blastn
[2024-01-24 14:39:59,410] [INFO] Running command: blastn -query GCF_006228385.1_ASM622838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2880edc3-4219-4b12-860c-cb4e1380b86f/dqc_reference/reference_markers.fasta -out GCF_006228385.1_ASM622838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:00,175] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:00,179] [INFO] Selected 17 target genomes.
[2024-01-24 14:40:00,179] [INFO] Target genome list was writen to GCF_006228385.1_ASM622838v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:00,187] [INFO] Task started: fastANI
[2024-01-24 14:40:00,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgaac702f8-0f2f-4489-a41d-7664edac83f3/GCF_006228385.1_ASM622838v1_genomic.fna.gz --refList GCF_006228385.1_ASM622838v1_genomic.fna/target_genomes.txt --output GCF_006228385.1_ASM622838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:13,368] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:13,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2880edc3-4219-4b12-860c-cb4e1380b86f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:13,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2880edc3-4219-4b12-860c-cb4e1380b86f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:13,378] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:13,378] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:13,378] [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
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	100.0	1384	1386	95	conclusive
Salinimonas profundi	strain=HHU 13199	GCA_014750655.1	2729140	2729140	type	True	85.5604	1121	1386	95	below_threshold
Salinimonas chungwhensis	strain=DSM 16280	GCA_000378185.1	265425	265425	type	True	80.8196	582	1386	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	79.7219	335	1386	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	78.9448	202	1386	95	below_threshold
Alteromonas confluentis	strain=KCTC 42603	GCA_001757105.1	1656094	1656094	type	True	78.919	184	1386	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	78.3671	148	1386	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	78.0466	154	1386	95	below_threshold
Alteromonas ponticola	strain=MYP5	GCA_012911815.1	2720613	2720613	type	True	78.0399	138	1386	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:13,380] [INFO] DFAST Taxonomy check result was written to GCF_006228385.1_ASM622838v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:13,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:13,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:13,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2880edc3-4219-4b12-860c-cb4e1380b86f/dqc_reference/checkm_data
[2024-01-24 14:40:13,383] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:13,425] [INFO] Task started: CheckM
[2024-01-24 14:40:13,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006228385.1_ASM622838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006228385.1_ASM622838v1_genomic.fna/checkm_input GCF_006228385.1_ASM622838v1_genomic.fna/checkm_result
[2024-01-24 14:40:48,989] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:48,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:49,019] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:49,020] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:49,020] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006228385.1_ASM622838v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:49,021] [INFO] Task started: Blastn
[2024-01-24 14:40:49,021] [INFO] Running command: blastn -query GCF_006228385.1_ASM622838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2880edc3-4219-4b12-860c-cb4e1380b86f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006228385.1_ASM622838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:50,215] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:50,219] [INFO] Selected 18 target genomes.
[2024-01-24 14:40:50,220] [INFO] Target genome list was writen to GCF_006228385.1_ASM622838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:50,235] [INFO] Task started: fastANI
[2024-01-24 14:40:50,236] [INFO] Running command: fastANI --query /var/lib/cwl/stgaac702f8-0f2f-4489-a41d-7664edac83f3/GCF_006228385.1_ASM622838v1_genomic.fna.gz --refList GCF_006228385.1_ASM622838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006228385.1_ASM622838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:04,600] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:04,678] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:04,678] [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_006228385.1	s__Alteromonas iocasae	100.0	1385	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014750655.1	s__Alteromonas profundi_A	85.5604	1121	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003429285.1	s__Alteromonas sediminis	80.8344	314	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.07	99.07	0.95	0.95	2	-
GCF_000378185.1	s__Alteromonas chungwhensis	80.8236	582	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003731635.1	s__Alteromonas oceani	79.99	200	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	79.7483	334	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903772925.1	s__Alteromonas macleodii_A	79.3886	147	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644725.1	s__Alteromonas sp015644725	79.0092	254	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651815.1	s__Alteromonas halophila	78.9285	202	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757105.1	s__Alteromonas confluentis	78.8627	183	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019249245.1	s__Alteromonas lipotrueiana	78.8354	241	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506055.1	s__Alteromonas lipotrueae	78.6436	151	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.66	99.49	0.97	0.95	4	-
GCF_001758465.1	s__Alteromonas lipolytica	78.3423	147	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_012911815.1	s__Alteromonas ponticola	78.0714	137	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339125.1	s__Alteromonas sp002335925	77.6308	156	1386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.57	96.36	0.89	0.83	19	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:04,680] [INFO] GTDB search result was written to GCF_006228385.1_ASM622838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:04,681] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:04,685] [INFO] DFAST_QC result json was written to GCF_006228385.1_ASM622838v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:04,686] [INFO] DFAST_QC completed!
[2024-01-24 14:41:04,686] [INFO] Total running time: 0h1m19s