[2024-01-24 11:51:06,756] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dbc5642-55cb-446e-95d5-e2f9df2d9f86/dqc_reference
[2024-01-24 11:51:08,065] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,066] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,067] [INFO] Running command: gunzip -c /var/lib/cwl/stg62384ac9-ee00-477f-abef-47206a6ea441/GCF_016592435.1_ASM1659243v1_genomic.fna.gz | prodigal -d GCF_016592435.1_ASM1659243v1_genomic.fna/cds.fna -a GCF_016592435.1_ASM1659243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:18,038] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:18,038] [INFO] Task started: HMMsearch
[2024-01-24 11:51:18,039] [INFO] Running command: hmmsearch --tblout GCF_016592435.1_ASM1659243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dbc5642-55cb-446e-95d5-e2f9df2d9f86/dqc_reference/reference_markers.hmm GCF_016592435.1_ASM1659243v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:18,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:18,350] [INFO] Found 6/6 markers.
[2024-01-24 11:51:18,390] [INFO] Query marker FASTA was written to GCF_016592435.1_ASM1659243v1_genomic.fna/markers.fasta
[2024-01-24 11:51:18,391] [INFO] Task started: Blastn
[2024-01-24 11:51:18,391] [INFO] Running command: blastn -query GCF_016592435.1_ASM1659243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dbc5642-55cb-446e-95d5-e2f9df2d9f86/dqc_reference/reference_markers.fasta -out GCF_016592435.1_ASM1659243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:19,008] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:19,012] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:19,012] [INFO] Target genome list was writen to GCF_016592435.1_ASM1659243v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:19,045] [INFO] Task started: fastANI
[2024-01-24 11:51:19,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg62384ac9-ee00-477f-abef-47206a6ea441/GCF_016592435.1_ASM1659243v1_genomic.fna.gz --refList GCF_016592435.1_ASM1659243v1_genomic.fna/target_genomes.txt --output GCF_016592435.1_ASM1659243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:30,406] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:30,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dbc5642-55cb-446e-95d5-e2f9df2d9f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:30,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dbc5642-55cb-446e-95d5-e2f9df2d9f86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:30,426] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:51:30,426] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:30,426] [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
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	100.0	1276	1277	95	conclusive
Amphritea japonica	strain=JCM 14782	GCA_024347275.1	452627	452627	type	True	99.9911	1275	1277	95	conclusive
Amphritea japonica	strain=JAMM 1866	GCA_000381785.1	452627	452627	type	True	99.9821	1254	1277	95	conclusive
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	79.8875	449	1277	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	79.7205	443	1277	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	79.261	543	1277	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	79.0919	531	1277	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	77.6149	76	1277	95	below_threshold
Neptuniibacter pectenicola	strain=LFT 1.8	GCA_001597735.1	1806669	1806669	type	True	77.5236	92	1277	95	below_threshold
Marinobacterium alkalitolerans	strain=AK62	GCA_017776525.1	1542925	1542925	type	True	76.8473	71	1277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:30,428] [INFO] DFAST Taxonomy check result was written to GCF_016592435.1_ASM1659243v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:30,428] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:30,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:30,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dbc5642-55cb-446e-95d5-e2f9df2d9f86/dqc_reference/checkm_data
[2024-01-24 11:51:30,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:30,470] [INFO] Task started: CheckM
[2024-01-24 11:51:30,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016592435.1_ASM1659243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016592435.1_ASM1659243v1_genomic.fna/checkm_input GCF_016592435.1_ASM1659243v1_genomic.fna/checkm_result
[2024-01-24 11:52:06,170] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:06,172] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:06,195] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:06,196] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:06,196] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016592435.1_ASM1659243v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:06,197] [INFO] Task started: Blastn
[2024-01-24 11:52:06,197] [INFO] Running command: blastn -query GCF_016592435.1_ASM1659243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dbc5642-55cb-446e-95d5-e2f9df2d9f86/dqc_reference/reference_markers_gtdb.fasta -out GCF_016592435.1_ASM1659243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:07,062] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:07,066] [INFO] Selected 11 target genomes.
[2024-01-24 11:52:07,066] [INFO] Target genome list was writen to GCF_016592435.1_ASM1659243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:07,078] [INFO] Task started: fastANI
[2024-01-24 11:52:07,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg62384ac9-ee00-477f-abef-47206a6ea441/GCF_016592435.1_ASM1659243v1_genomic.fna.gz --refList GCF_016592435.1_ASM1659243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016592435.1_ASM1659243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:15,813] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:15,825] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:15,825] [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_016592435.1	s__Amphritea japonica	100.0	1276	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_016744155.1	s__Amphritea sp016744155	83.446	972	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067325.1	s__Amphritea sp018067325	83.3372	660	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	-
GCF_003858655.1	s__Amphritea balenae	79.8824	449	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018223185.1	s__Amphritea sp018223185	79.3711	534	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.96	99.96	0.97	0.97	2	-
GCF_900111095.1	s__Amphritea atlantica	79.2791	541	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860855.1	s__Amphritea atlantica_A	79.2105	392	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016924235.1	s__Amphritea sp016924235	79.1467	521	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_001597735.1	s__Neptuniibacter pectenicola	77.5345	93	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	98.78	98.78	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:15,827] [INFO] GTDB search result was written to GCF_016592435.1_ASM1659243v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:15,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:15,832] [INFO] DFAST_QC result json was written to GCF_016592435.1_ASM1659243v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:15,833] [INFO] DFAST_QC completed!
[2024-01-24 11:52:15,833] [INFO] Total running time: 0h1m9s