[2024-01-24 13:01:38,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:38,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:38,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c3cf35f-a369-476b-ab7a-4115bad35add/dqc_reference
[2024-01-24 13:01:40,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:40,904] [INFO] Task started: Prodigal
[2024-01-24 13:01:40,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg7da84a4a-e364-4167-8fc1-bd04b8b5217e/GCF_004362745.1_ASM436274v1_genomic.fna.gz | prodigal -d GCF_004362745.1_ASM436274v1_genomic.fna/cds.fna -a GCF_004362745.1_ASM436274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:53,794] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:53,794] [INFO] Task started: HMMsearch
[2024-01-24 13:01:53,794] [INFO] Running command: hmmsearch --tblout GCF_004362745.1_ASM436274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c3cf35f-a369-476b-ab7a-4115bad35add/dqc_reference/reference_markers.hmm GCF_004362745.1_ASM436274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:54,170] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:54,172] [INFO] Found 6/6 markers.
[2024-01-24 13:01:54,242] [INFO] Query marker FASTA was written to GCF_004362745.1_ASM436274v1_genomic.fna/markers.fasta
[2024-01-24 13:01:54,243] [INFO] Task started: Blastn
[2024-01-24 13:01:54,243] [INFO] Running command: blastn -query GCF_004362745.1_ASM436274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c3cf35f-a369-476b-ab7a-4115bad35add/dqc_reference/reference_markers.fasta -out GCF_004362745.1_ASM436274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:55,556] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:55,560] [INFO] Selected 13 target genomes.
[2024-01-24 13:01:55,561] [INFO] Target genome list was writen to GCF_004362745.1_ASM436274v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:55,567] [INFO] Task started: fastANI
[2024-01-24 13:01:55,567] [INFO] Running command: fastANI --query /var/lib/cwl/stg7da84a4a-e364-4167-8fc1-bd04b8b5217e/GCF_004362745.1_ASM436274v1_genomic.fna.gz --refList GCF_004362745.1_ASM436274v1_genomic.fna/target_genomes.txt --output GCF_004362745.1_ASM436274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:13,964] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:13,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c3cf35f-a369-476b-ab7a-4115bad35add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:13,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c3cf35f-a369-476b-ab7a-4115bad35add/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:13,978] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:13,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:13,978] [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
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	100.0	1658	1658	95	conclusive
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	99.6373	1215	1658	95	conclusive
Chthonobacter albigriseus	strain=KCTC 42450	GCA_013839445.1	1683161	1683161	type	True	81.1267	830	1658	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	80.7853	870	1658	95	below_threshold
Pleomorphomonas koreensis	strain=DSM 23070	GCA_000425185.1	257440	257440	type	True	80.2223	751	1658	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	80.0133	771	1658	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.2877	603	1658	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	77.8819	626	1658	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.7575	701	1658	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.7161	750	1658	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	77.4915	641	1658	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	77.4443	560	1658	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.3911	527	1658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:13,980] [INFO] DFAST Taxonomy check result was written to GCF_004362745.1_ASM436274v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:13,981] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:13,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:13,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c3cf35f-a369-476b-ab7a-4115bad35add/dqc_reference/checkm_data
[2024-01-24 13:02:13,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:14,043] [INFO] Task started: CheckM
[2024-01-24 13:02:14,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362745.1_ASM436274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362745.1_ASM436274v1_genomic.fna/checkm_input GCF_004362745.1_ASM436274v1_genomic.fna/checkm_result
[2024-01-24 13:03:01,709] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:01,710] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:01,746] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:01,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:01,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362745.1_ASM436274v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:01,748] [INFO] Task started: Blastn
[2024-01-24 13:03:01,748] [INFO] Running command: blastn -query GCF_004362745.1_ASM436274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c3cf35f-a369-476b-ab7a-4115bad35add/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362745.1_ASM436274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:04,124] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:04,129] [INFO] Selected 8 target genomes.
[2024-01-24 13:03:04,130] [INFO] Target genome list was writen to GCF_004362745.1_ASM436274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:04,152] [INFO] Task started: fastANI
[2024-01-24 13:03:04,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg7da84a4a-e364-4167-8fc1-bd04b8b5217e/GCF_004362745.1_ASM436274v1_genomic.fna.gz --refList GCF_004362745.1_ASM436274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362745.1_ASM436274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:15,665] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:15,682] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:15,683] [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_004362745.1	s__Oharaeibacter diazotrophicus	100.0	1657	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	conclusive
GCF_013839445.1	s__Chthonobacter albigriseus	81.2038	819	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839525.1	s__Mongoliimonas rhizosphaerae	80.978	882	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927285.1	s__Mongoliimonas terrestris	80.8364	912	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Mongoliimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015904235.1	s__L22 sp015904235	80.8207	862	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425185.1	s__Pleomorphomonas koreensis	80.2218	751	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	95.03	95.03	0.88	0.88	2	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	80.0445	768	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCF_016653355.1	s__Rhodoplanes elegans	77.465	650	1658	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:15,685] [INFO] GTDB search result was written to GCF_004362745.1_ASM436274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:15,686] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:15,690] [INFO] DFAST_QC result json was written to GCF_004362745.1_ASM436274v1_genomic.fna/dqc_result.json
[2024-01-24 13:03:15,691] [INFO] DFAST_QC completed!
[2024-01-24 13:03:15,691] [INFO] Total running time: 0h1m38s