[2024-01-24 12:53:36,651] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:36,655] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:36,656] [INFO] DQC Reference Directory: /var/lib/cwl/stg16b5b185-323c-4b6b-82d8-5f27b25c61ee/dqc_reference
[2024-01-24 12:53:39,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:39,888] [INFO] Task started: Prodigal
[2024-01-24 12:53:39,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg314a4d64-6f5d-4a3f-a9f8-0d39cba822fe/GCF_008064665.1_ASM806466v1_genomic.fna.gz | prodigal -d GCF_008064665.1_ASM806466v1_genomic.fna/cds.fna -a GCF_008064665.1_ASM806466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:55,100] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:55,100] [INFO] Task started: HMMsearch
[2024-01-24 12:53:55,100] [INFO] Running command: hmmsearch --tblout GCF_008064665.1_ASM806466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16b5b185-323c-4b6b-82d8-5f27b25c61ee/dqc_reference/reference_markers.hmm GCF_008064665.1_ASM806466v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:55,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:55,422] [INFO] Found 6/6 markers.
[2024-01-24 12:53:55,468] [INFO] Query marker FASTA was written to GCF_008064665.1_ASM806466v1_genomic.fna/markers.fasta
[2024-01-24 12:53:55,468] [INFO] Task started: Blastn
[2024-01-24 12:53:55,468] [INFO] Running command: blastn -query GCF_008064665.1_ASM806466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16b5b185-323c-4b6b-82d8-5f27b25c61ee/dqc_reference/reference_markers.fasta -out GCF_008064665.1_ASM806466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:58,208] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:58,213] [INFO] Selected 14 target genomes.
[2024-01-24 12:53:58,213] [INFO] Target genome list was writen to GCF_008064665.1_ASM806466v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:58,220] [INFO] Task started: fastANI
[2024-01-24 12:53:58,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg314a4d64-6f5d-4a3f-a9f8-0d39cba822fe/GCF_008064665.1_ASM806466v1_genomic.fna.gz --refList GCF_008064665.1_ASM806466v1_genomic.fna/target_genomes.txt --output GCF_008064665.1_ASM806466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:10,831] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:10,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16b5b185-323c-4b6b-82d8-5f27b25c61ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:10,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16b5b185-323c-4b6b-82d8-5f27b25c61ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:10,869] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:10,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:10,870] [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
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	100.0	1604	1604	95	conclusive
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	81.8795	856	1604	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	81.8145	823	1604	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.7941	459	1604	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.3918	339	1604	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	78.2978	345	1604	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	77.9184	264	1604	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.9144	261	1604	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	77.7881	328	1604	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	77.7498	312	1604	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	77.1717	116	1604	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.8571	192	1604	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.8211	194	1604	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.7232	158	1604	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:10,872] [INFO] DFAST Taxonomy check result was written to GCF_008064665.1_ASM806466v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:10,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:10,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:10,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16b5b185-323c-4b6b-82d8-5f27b25c61ee/dqc_reference/checkm_data
[2024-01-24 12:54:10,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:10,926] [INFO] Task started: CheckM
[2024-01-24 12:54:10,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008064665.1_ASM806466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008064665.1_ASM806466v1_genomic.fna/checkm_input GCF_008064665.1_ASM806466v1_genomic.fna/checkm_result
[2024-01-24 12:54:56,026] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:56,027] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:56,052] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:56,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:56,053] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008064665.1_ASM806466v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:56,053] [INFO] Task started: Blastn
[2024-01-24 12:54:56,053] [INFO] Running command: blastn -query GCF_008064665.1_ASM806466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16b5b185-323c-4b6b-82d8-5f27b25c61ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_008064665.1_ASM806466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:58,312] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:58,317] [INFO] Selected 9 target genomes.
[2024-01-24 12:54:58,318] [INFO] Target genome list was writen to GCF_008064665.1_ASM806466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:58,325] [INFO] Task started: fastANI
[2024-01-24 12:54:58,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg314a4d64-6f5d-4a3f-a9f8-0d39cba822fe/GCF_008064665.1_ASM806466v1_genomic.fna.gz --refList GCF_008064665.1_ASM806466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008064665.1_ASM806466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:08,036] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:08,084] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:08,084] [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_008064665.1	s__Parahaliea maris	100.0	1604	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003402235.1	s__Parahaliea mediterranea	81.8802	855	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	81.8234	822	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	80.766	752	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	78.9907	427	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669285.1	s__Kineobactrum salinum	78.2864	346	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	78.2764	346	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	77.9144	261	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_000423125.1	s__Haliea salexigens	77.7881	328	1604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:08,086] [INFO] GTDB search result was written to GCF_008064665.1_ASM806466v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:08,087] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:08,090] [INFO] DFAST_QC result json was written to GCF_008064665.1_ASM806466v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:08,090] [INFO] DFAST_QC completed!
[2024-01-24 12:55:08,090] [INFO] Total running time: 0h1m31s