[2024-01-24 11:34:43,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg79281814-5c2a-4f14-a87f-1e2aea8c380d/dqc_reference
[2024-01-24 11:34:44,481] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,482] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,483] [INFO] Running command: gunzip -c /var/lib/cwl/stge3799701-b8da-41a4-b367-8c6b676e0aeb/GCF_002903165.1_ASM290316v1_genomic.fna.gz | prodigal -d GCF_002903165.1_ASM290316v1_genomic.fna/cds.fna -a GCF_002903165.1_ASM290316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:57,232] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:57,233] [INFO] Task started: HMMsearch
[2024-01-24 11:34:57,233] [INFO] Running command: hmmsearch --tblout GCF_002903165.1_ASM290316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79281814-5c2a-4f14-a87f-1e2aea8c380d/dqc_reference/reference_markers.hmm GCF_002903165.1_ASM290316v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:57,555] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:57,557] [INFO] Found 6/6 markers.
[2024-01-24 11:34:57,610] [INFO] Query marker FASTA was written to GCF_002903165.1_ASM290316v1_genomic.fna/markers.fasta
[2024-01-24 11:34:57,611] [INFO] Task started: Blastn
[2024-01-24 11:34:57,611] [INFO] Running command: blastn -query GCF_002903165.1_ASM290316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79281814-5c2a-4f14-a87f-1e2aea8c380d/dqc_reference/reference_markers.fasta -out GCF_002903165.1_ASM290316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:58,532] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:58,537] [INFO] Selected 11 target genomes.
[2024-01-24 11:34:58,539] [INFO] Target genome list was writen to GCF_002903165.1_ASM290316v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:58,545] [INFO] Task started: fastANI
[2024-01-24 11:34:58,545] [INFO] Running command: fastANI --query /var/lib/cwl/stge3799701-b8da-41a4-b367-8c6b676e0aeb/GCF_002903165.1_ASM290316v1_genomic.fna.gz --refList GCF_002903165.1_ASM290316v1_genomic.fna/target_genomes.txt --output GCF_002903165.1_ASM290316v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:08,070] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:08,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79281814-5c2a-4f14-a87f-1e2aea8c380d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:08,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79281814-5c2a-4f14-a87f-1e2aea8c380d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:08,085] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:08,085] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:08,085] [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
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	100.0	1350	1353	95	conclusive
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	99.9982	1351	1353	95	conclusive
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	87.5898	1025	1353	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	87.5585	1014	1353	95	below_threshold
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	83.8394	905	1353	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	83.7226	891	1353	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	78.415	362	1353	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	78.3331	363	1353	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	78.2657	366	1353	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	78.2074	336	1353	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	78.167	336	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:08,087] [INFO] DFAST Taxonomy check result was written to GCF_002903165.1_ASM290316v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:08,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:08,087] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:08,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79281814-5c2a-4f14-a87f-1e2aea8c380d/dqc_reference/checkm_data
[2024-01-24 11:35:08,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:08,129] [INFO] Task started: CheckM
[2024-01-24 11:35:08,129] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002903165.1_ASM290316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002903165.1_ASM290316v1_genomic.fna/checkm_input GCF_002903165.1_ASM290316v1_genomic.fna/checkm_result
[2024-01-24 11:35:47,353] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:47,354] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:47,372] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:47,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:47,373] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002903165.1_ASM290316v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:47,373] [INFO] Task started: Blastn
[2024-01-24 11:35:47,373] [INFO] Running command: blastn -query GCF_002903165.1_ASM290316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg79281814-5c2a-4f14-a87f-1e2aea8c380d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002903165.1_ASM290316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:48,902] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:48,905] [INFO] Selected 6 target genomes.
[2024-01-24 11:35:48,905] [INFO] Target genome list was writen to GCF_002903165.1_ASM290316v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:48,910] [INFO] Task started: fastANI
[2024-01-24 11:35:48,910] [INFO] Running command: fastANI --query /var/lib/cwl/stge3799701-b8da-41a4-b367-8c6b676e0aeb/GCF_002903165.1_ASM290316v1_genomic.fna.gz --refList GCF_002903165.1_ASM290316v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002903165.1_ASM290316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:54,628] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:54,634] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:54,634] [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_002903165.1	s__Pseudomonas_D oceani	100.0	1350	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002197985.1	s__Pseudomonas_D aestusnigri	87.5349	1016	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	84.6666	937	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCF_900114765.1	s__Pseudomonas_D pachastrellae	83.8301	906	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCA_002296055.1	s__Pseudomonas_D sp002296055	82.5449	694	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105255.1	s__Pseudomonas_D sabulinigri	80.6919	686	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:54,636] [INFO] GTDB search result was written to GCF_002903165.1_ASM290316v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:54,636] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:54,639] [INFO] DFAST_QC result json was written to GCF_002903165.1_ASM290316v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:54,639] [INFO] DFAST_QC completed!
[2024-01-24 11:35:54,639] [INFO] Total running time: 0h1m12s