[2024-01-25 19:43:35,337] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:35,338] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:35,338] [INFO] DQC Reference Directory: /var/lib/cwl/stg5330f016-4085-43ca-8af6-bafcb8d3b1ce/dqc_reference
[2024-01-25 19:43:36,501] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:36,502] [INFO] Task started: Prodigal
[2024-01-25 19:43:36,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg3324423e-39db-4ab7-bfb2-7f94a0c46594/GCF_002807685.1_ASM280768v1_genomic.fna.gz | prodigal -d GCF_002807685.1_ASM280768v1_genomic.fna/cds.fna -a GCF_002807685.1_ASM280768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:44,572] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:44,572] [INFO] Task started: HMMsearch
[2024-01-25 19:43:44,572] [INFO] Running command: hmmsearch --tblout GCF_002807685.1_ASM280768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5330f016-4085-43ca-8af6-bafcb8d3b1ce/dqc_reference/reference_markers.hmm GCF_002807685.1_ASM280768v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:44,804] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:44,805] [INFO] Found 6/6 markers.
[2024-01-25 19:43:44,834] [INFO] Query marker FASTA was written to GCF_002807685.1_ASM280768v1_genomic.fna/markers.fasta
[2024-01-25 19:43:44,834] [INFO] Task started: Blastn
[2024-01-25 19:43:44,834] [INFO] Running command: blastn -query GCF_002807685.1_ASM280768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5330f016-4085-43ca-8af6-bafcb8d3b1ce/dqc_reference/reference_markers.fasta -out GCF_002807685.1_ASM280768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:45,489] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:45,492] [INFO] Selected 24 target genomes.
[2024-01-25 19:43:45,492] [INFO] Target genome list was writen to GCF_002807685.1_ASM280768v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:45,530] [INFO] Task started: fastANI
[2024-01-25 19:43:45,530] [INFO] Running command: fastANI --query /var/lib/cwl/stg3324423e-39db-4ab7-bfb2-7f94a0c46594/GCF_002807685.1_ASM280768v1_genomic.fna.gz --refList GCF_002807685.1_ASM280768v1_genomic.fna/target_genomes.txt --output GCF_002807685.1_ASM280768v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:01,673] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:01,674] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5330f016-4085-43ca-8af6-bafcb8d3b1ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:01,674] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5330f016-4085-43ca-8af6-bafcb8d3b1ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:01,682] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:01,682] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:01,682] [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
Alteromonas flava	strain=P0211	GCA_002807685.1	2048003	2048003	type	True	100.0	1200	1201	95	conclusive
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	79.6864	325	1201	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	78.9315	81	1201	95	below_threshold
Alteromonas sediminis	strain=U0105	GCA_003820355.1	2259342	2259342	type	True	78.4562	77	1201	95	below_threshold
Alteromonas oceanisediminis	strain=SM 2104	GCA_018474025.1	2836180	2836180	type	True	78.4379	147	1201	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.2984	90	1201	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	78.1142	87	1201	95	below_threshold
Alteromonas genovensis	strain=LMG 24078	GCA_010500895.1	471225	471225	type	True	77.819	83	1201	95	below_threshold
Paraneptunicella aestuarii	strain=NBU2194	GCA_019900845.1	2831148	2831148	type	True	77.7229	57	1201	95	below_threshold
Alteromonas halophila	strain=KCTC 22164	GCA_014651815.1	516698	516698	type	True	77.7073	74	1201	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	77.6086	84	1201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:01,683] [INFO] DFAST Taxonomy check result was written to GCF_002807685.1_ASM280768v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:01,684] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:01,684] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:01,684] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5330f016-4085-43ca-8af6-bafcb8d3b1ce/dqc_reference/checkm_data
[2024-01-25 19:44:01,685] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:01,723] [INFO] Task started: CheckM
[2024-01-25 19:44:01,723] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002807685.1_ASM280768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002807685.1_ASM280768v1_genomic.fna/checkm_input GCF_002807685.1_ASM280768v1_genomic.fna/checkm_result
[2024-01-25 19:44:29,425] [INFO] Task succeeded: CheckM
[2024-01-25 19:44:29,426] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:44:29,443] [INFO] ===== Completeness check finished =====
[2024-01-25 19:44:29,444] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:44:29,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002807685.1_ASM280768v1_genomic.fna/markers.fasta)
[2024-01-25 19:44:29,444] [INFO] Task started: Blastn
[2024-01-25 19:44:29,445] [INFO] Running command: blastn -query GCF_002807685.1_ASM280768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5330f016-4085-43ca-8af6-bafcb8d3b1ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_002807685.1_ASM280768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:30,511] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:30,514] [INFO] Selected 23 target genomes.
[2024-01-25 19:44:30,514] [INFO] Target genome list was writen to GCF_002807685.1_ASM280768v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:44:30,569] [INFO] Task started: fastANI
[2024-01-25 19:44:30,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg3324423e-39db-4ab7-bfb2-7f94a0c46594/GCF_002807685.1_ASM280768v1_genomic.fna.gz --refList GCF_002807685.1_ASM280768v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002807685.1_ASM280768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:44:46,487] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:46,497] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:44:46,497] [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_002807685.1	s__Alteromonas_E flava	100.0	1200	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002807665.1	s__Alteromonas_E facilis	79.6709	326	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993325.1	s__Alteromonas gracilis	78.9581	81	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	96.94	96.21	0.87	0.84	4	-
GCF_003820355.1	s__Alteromonas_F sediminis	78.4747	76	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018474025.1	s__Alteromonas_E sp018474025	78.4068	147	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953635.1	s__Alteromonas abrolhosensis	78.3409	89	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_900129565.1	s__Alteromonas aggregata	78.27	89	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.34	96.39	0.91	0.85	11	-
GCF_001758465.1	s__Alteromonas lipolytica	78.1142	87	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_006538345.1	s__Alteromonas sp006538345	78.1017	84	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016405965.1	s__Alteromonas sp016405965	78.0597	75	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016756315.1	s__Alteromonas sp009811495	77.9096	100	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.33	96.67	0.93	0.86	3	-
GCF_903772925.1	s__Alteromonas macleodii_A	77.9032	97	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018100795.1	s__Alteromonas sp018100795	77.877	90	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500895.1	s__Alteromonas genovensis	77.819	83	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.09	98.06	0.82	0.81	3	-
GCF_014651815.1	s__Alteromonas halophila	77.7073	74	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753865.1	s__Alteromonas sp000753865	77.6487	86	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:44:46,499] [INFO] GTDB search result was written to GCF_002807685.1_ASM280768v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:44:46,499] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:44:46,502] [INFO] DFAST_QC result json was written to GCF_002807685.1_ASM280768v1_genomic.fna/dqc_result.json
[2024-01-25 19:44:46,502] [INFO] DFAST_QC completed!
[2024-01-25 19:44:46,502] [INFO] Total running time: 0h1m11s