[2024-01-24 12:05:58,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:58,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:58,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg5155861c-9be5-49b9-9f8d-1beac7ea68e3/dqc_reference
[2024-01-24 12:06:00,296] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:00,297] [INFO] Task started: Prodigal
[2024-01-24 12:06:00,297] [INFO] Running command: gunzip -c /var/lib/cwl/stg96860c8e-86ac-4c86-8f91-a0676646e951/GCF_002786285.1_ASM278628v1_genomic.fna.gz | prodigal -d GCF_002786285.1_ASM278628v1_genomic.fna/cds.fna -a GCF_002786285.1_ASM278628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:13,577] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:13,577] [INFO] Task started: HMMsearch
[2024-01-24 12:06:13,578] [INFO] Running command: hmmsearch --tblout GCF_002786285.1_ASM278628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5155861c-9be5-49b9-9f8d-1beac7ea68e3/dqc_reference/reference_markers.hmm GCF_002786285.1_ASM278628v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:13,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:13,916] [INFO] Found 6/6 markers.
[2024-01-24 12:06:13,956] [INFO] Query marker FASTA was written to GCF_002786285.1_ASM278628v1_genomic.fna/markers.fasta
[2024-01-24 12:06:13,957] [INFO] Task started: Blastn
[2024-01-24 12:06:13,957] [INFO] Running command: blastn -query GCF_002786285.1_ASM278628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5155861c-9be5-49b9-9f8d-1beac7ea68e3/dqc_reference/reference_markers.fasta -out GCF_002786285.1_ASM278628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:15,091] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:15,095] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:15,095] [INFO] Target genome list was writen to GCF_002786285.1_ASM278628v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:15,100] [INFO] Task started: fastANI
[2024-01-24 12:06:15,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg96860c8e-86ac-4c86-8f91-a0676646e951/GCF_002786285.1_ASM278628v1_genomic.fna.gz --refList GCF_002786285.1_ASM278628v1_genomic.fna/target_genomes.txt --output GCF_002786285.1_ASM278628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:25,837] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:25,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5155861c-9be5-49b9-9f8d-1beac7ea68e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:25,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5155861c-9be5-49b9-9f8d-1beac7ea68e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:25,848] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:25,849] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:25,849] [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
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	100.0	1417	1423	95	conclusive
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	99.9883	1399	1423	95	conclusive
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	83.9702	969	1423	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	83.9398	968	1423	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	81.6201	787	1423	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	80.4301	653	1423	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	79.2081	570	1423	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.9579	569	1423	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.8601	498	1423	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.1828	439	1423	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.6116	364	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:25,851] [INFO] DFAST Taxonomy check result was written to GCF_002786285.1_ASM278628v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:25,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:25,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:25,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5155861c-9be5-49b9-9f8d-1beac7ea68e3/dqc_reference/checkm_data
[2024-01-24 12:06:25,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:25,897] [INFO] Task started: CheckM
[2024-01-24 12:06:25,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002786285.1_ASM278628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002786285.1_ASM278628v1_genomic.fna/checkm_input GCF_002786285.1_ASM278628v1_genomic.fna/checkm_result
[2024-01-24 12:07:06,869] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:06,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:06,892] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:06,892] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:06,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002786285.1_ASM278628v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:06,893] [INFO] Task started: Blastn
[2024-01-24 12:07:06,893] [INFO] Running command: blastn -query GCF_002786285.1_ASM278628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5155861c-9be5-49b9-9f8d-1beac7ea68e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002786285.1_ASM278628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:09,005] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:09,009] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:09,010] [INFO] Target genome list was writen to GCF_002786285.1_ASM278628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:09,014] [INFO] Task started: fastANI
[2024-01-24 12:07:09,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg96860c8e-86ac-4c86-8f91-a0676646e951/GCF_002786285.1_ASM278628v1_genomic.fna.gz --refList GCF_002786285.1_ASM278628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002786285.1_ASM278628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:16,634] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:16,648] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:16,648] [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_900215355.1	s__Pseudooceanicola antarcticus	99.9883	1399	1423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000220565.1	s__Pseudooceanicola sp000220565	87.9394	988	1423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	87.7213	1095	1423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_002786295.1	s__Pseudooceanicola marinus	83.9539	971	1423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	81.5883	771	1423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	81.365	758	1423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	80.4534	654	1423	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:16,650] [INFO] GTDB search result was written to GCF_002786285.1_ASM278628v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:16,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:16,653] [INFO] DFAST_QC result json was written to GCF_002786285.1_ASM278628v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:16,653] [INFO] DFAST_QC completed!
[2024-01-24 12:07:16,653] [INFO] Total running time: 0h1m18s