[2023-06-18 20:30:04,101] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:30:04,105] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:30:04,105] [INFO] DQC Reference Directory: /var/lib/cwl/stg97ea1df6-794c-4cb9-9c7b-dc965156b04a/dqc_reference
[2023-06-18 20:30:05,352] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:30:05,354] [INFO] Task started: Prodigal
[2023-06-18 20:30:05,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg5502c702-79a8-4fee-83e2-9368847111ed/GCA_018067325.1_ASM1806732v1_genomic.fna.gz | prodigal -d GCA_018067325.1_ASM1806732v1_genomic.fna/cds.fna -a GCA_018067325.1_ASM1806732v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:30:11,528] [INFO] Task succeeded: Prodigal
[2023-06-18 20:30:11,529] [INFO] Task started: HMMsearch
[2023-06-18 20:30:11,529] [INFO] Running command: hmmsearch --tblout GCA_018067325.1_ASM1806732v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97ea1df6-794c-4cb9-9c7b-dc965156b04a/dqc_reference/reference_markers.hmm GCA_018067325.1_ASM1806732v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:30:11,785] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:30:11,787] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5502c702-79a8-4fee-83e2-9368847111ed/GCA_018067325.1_ASM1806732v1_genomic.fna.gz]
[2023-06-18 20:30:11,823] [INFO] Query marker FASTA was written to GCA_018067325.1_ASM1806732v1_genomic.fna/markers.fasta
[2023-06-18 20:30:11,824] [INFO] Task started: Blastn
[2023-06-18 20:30:11,824] [INFO] Running command: blastn -query GCA_018067325.1_ASM1806732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97ea1df6-794c-4cb9-9c7b-dc965156b04a/dqc_reference/reference_markers.fasta -out GCA_018067325.1_ASM1806732v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:12,498] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:12,502] [INFO] Selected 15 target genomes.
[2023-06-18 20:30:12,503] [INFO] Target genome list was writen to GCA_018067325.1_ASM1806732v1_genomic.fna/target_genomes.txt
[2023-06-18 20:30:12,504] [INFO] Task started: fastANI
[2023-06-18 20:30:12,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg5502c702-79a8-4fee-83e2-9368847111ed/GCA_018067325.1_ASM1806732v1_genomic.fna.gz --refList GCA_018067325.1_ASM1806732v1_genomic.fna/target_genomes.txt --output GCA_018067325.1_ASM1806732v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:30:23,442] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:23,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97ea1df6-794c-4cb9-9c7b-dc965156b04a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:30:23,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97ea1df6-794c-4cb9-9c7b-dc965156b04a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:30:23,457] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:30:23,457] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:30:23,457] [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=JCM 14782	GCA_024347275.1	452627	452627	type	True	83.5077	671	854	95	below_threshold
Amphritea japonica	strain=ATCC BAA-1530	GCA_016592435.1	452627	452627	type	True	83.4792	665	854	95	below_threshold
Amphritea japonica	strain=JAMM 1866	GCA_000381785.1	452627	452627	type	True	83.3953	668	854	95	below_threshold
Amphritea balenae	strain=JAMM 1525	GCA_003858655.1	452629	452629	type	True	79.6494	292	854	95	below_threshold
Amphritea balenae	strain=JCM 14781	GCA_014646975.1	452629	452629	type	True	79.6423	289	854	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	79.5013	369	854	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	79.3989	382	854	95	below_threshold
Amphritea opalescens	strain=ANRC-JH13	GCA_003957515.1	2490544	2490544	type	True	79.2422	290	854	95	below_threshold
Amphritea ceti	strain=KCTC 42154	GCA_024347215.1	1524258	1524258	type	True	78.5953	117	854	95	below_threshold
Neptuniibacter marinus	strain=ATR 1.1	GCA_001597725.1	1806670	1806670	type	True	77.2812	66	854	95	below_threshold
Marinobacterium stanieri	strain=DSM 7027	GCA_900155945.1	49186	49186	type	True	76.9733	77	854	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.6842	62	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:30:23,461] [INFO] DFAST Taxonomy check result was written to GCA_018067325.1_ASM1806732v1_genomic.fna/tc_result.tsv
[2023-06-18 20:30:23,462] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:30:23,462] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:30:23,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97ea1df6-794c-4cb9-9c7b-dc965156b04a/dqc_reference/checkm_data
[2023-06-18 20:30:23,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:30:23,511] [INFO] Task started: CheckM
[2023-06-18 20:30:23,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018067325.1_ASM1806732v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018067325.1_ASM1806732v1_genomic.fna/checkm_input GCA_018067325.1_ASM1806732v1_genomic.fna/checkm_result
[2023-06-18 20:30:49,675] [INFO] Task succeeded: CheckM
[2023-06-18 20:30:49,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 20:30:49,707] [INFO] ===== Completeness check finished =====
[2023-06-18 20:30:49,707] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:30:49,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018067325.1_ASM1806732v1_genomic.fna/markers.fasta)
[2023-06-18 20:30:49,708] [INFO] Task started: Blastn
[2023-06-18 20:30:49,708] [INFO] Running command: blastn -query GCA_018067325.1_ASM1806732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97ea1df6-794c-4cb9-9c7b-dc965156b04a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018067325.1_ASM1806732v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:50,745] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:50,749] [INFO] Selected 10 target genomes.
[2023-06-18 20:30:50,749] [INFO] Target genome list was writen to GCA_018067325.1_ASM1806732v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:30:50,755] [INFO] Task started: fastANI
[2023-06-18 20:30:50,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg5502c702-79a8-4fee-83e2-9368847111ed/GCA_018067325.1_ASM1806732v1_genomic.fna.gz --refList GCA_018067325.1_ASM1806732v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018067325.1_ASM1806732v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:30:58,080] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:58,093] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:30:58,093] [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
GCA_018067325.1	s__Amphritea sp018067325	100.0	843	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.51	99.51	0.92	0.92	2	conclusive
GCA_016744155.1	s__Amphritea sp016744155	94.9529	787	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016592435.1	s__Amphritea japonica	83.4716	666	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003858655.1	s__Amphritea balenae	79.6494	292	854	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	79.6458	379	854	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	79.3989	382	854	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	79.3474	293	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957515.1	s__Amphritea opalescens	79.2355	291	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001597725.1	s__Neptuniibacter marinus	77.2812	66	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Neptuniibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155945.1	s__Marinobacterium stanieri	76.9418	78	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	96.47	96.47	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-06-18 20:30:58,095] [INFO] GTDB search result was written to GCA_018067325.1_ASM1806732v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:30:58,096] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:30:58,099] [INFO] DFAST_QC result json was written to GCA_018067325.1_ASM1806732v1_genomic.fna/dqc_result.json
[2023-06-18 20:30:58,099] [INFO] DFAST_QC completed!
[2023-06-18 20:30:58,100] [INFO] Total running time: 0h0m54s