[2024-01-25 20:19:35,560] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:35,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:35,562] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0e6b005-b388-48a3-ae55-6d89083b6a34/dqc_reference
[2024-01-25 20:19:36,783] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:36,783] [INFO] Task started: Prodigal
[2024-01-25 20:19:36,784] [INFO] Running command: gunzip -c /var/lib/cwl/stgda0afec9-78fd-4fce-bdc8-f60ffec2f540/GCF_014635845.1_ASM1463584v1_genomic.fna.gz | prodigal -d GCF_014635845.1_ASM1463584v1_genomic.fna/cds.fna -a GCF_014635845.1_ASM1463584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:45,457] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:45,458] [INFO] Task started: HMMsearch
[2024-01-25 20:19:45,458] [INFO] Running command: hmmsearch --tblout GCF_014635845.1_ASM1463584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0e6b005-b388-48a3-ae55-6d89083b6a34/dqc_reference/reference_markers.hmm GCF_014635845.1_ASM1463584v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:45,687] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:45,688] [INFO] Found 6/6 markers.
[2024-01-25 20:19:45,715] [INFO] Query marker FASTA was written to GCF_014635845.1_ASM1463584v1_genomic.fna/markers.fasta
[2024-01-25 20:19:45,715] [INFO] Task started: Blastn
[2024-01-25 20:19:45,716] [INFO] Running command: blastn -query GCF_014635845.1_ASM1463584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0e6b005-b388-48a3-ae55-6d89083b6a34/dqc_reference/reference_markers.fasta -out GCF_014635845.1_ASM1463584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:46,661] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:46,663] [INFO] Selected 24 target genomes.
[2024-01-25 20:19:46,664] [INFO] Target genome list was writen to GCF_014635845.1_ASM1463584v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:46,696] [INFO] Task started: fastANI
[2024-01-25 20:19:46,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgda0afec9-78fd-4fce-bdc8-f60ffec2f540/GCF_014635845.1_ASM1463584v1_genomic.fna.gz --refList GCF_014635845.1_ASM1463584v1_genomic.fna/target_genomes.txt --output GCF_014635845.1_ASM1463584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:20:07,985] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:07,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0e6b005-b388-48a3-ae55-6d89083b6a34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:20:07,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0e6b005-b388-48a3-ae55-6d89083b6a34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:20:08,005] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:20:08,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:20:08,006] [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
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	100.0	1009	1009	95	conclusive
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	82.3107	656	1009	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	79.6182	382	1009	95	below_threshold
Herbaspirillum chlorophenolicum	strain=CPW301	GCA_001189955.1	211589	211589	type	True	79.5844	384	1009	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.5494	429	1009	95	below_threshold
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	79.5206	387	1009	95	below_threshold
Noviherbaspirillum cavernae	strain=K2R10-39	GCA_003590875.1	2320862	2320862	type	True	79.4349	410	1009	95	below_threshold
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	79.2913	437	1009	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	79.2821	405	1009	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	79.2763	381	1009	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	79.2498	375	1009	95	below_threshold
Noviherbaspirillum aerium	strain=122213-3	GCA_008929045.1	2588497	2588497	type	True	79.2242	418	1009	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	79.2175	407	1009	95	below_threshold
Noviherbaspirillum denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	79.2	401	1009	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	79.1705	376	1009	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	78.8778	379	1009	95	below_threshold
Massilia niastensis	strain=DSM 21313	GCA_000382345.1	544911	544911	type	True	78.8406	410	1009	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	78.8342	364	1009	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	78.7579	363	1009	95	below_threshold
Massilia rhizosphaerae	strain=NEAU-GH312	GCA_016093545.1	2784389	2784389	type	True	78.713	403	1009	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	78.5978	366	1009	95	below_threshold
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	78.5875	432	1009	95	below_threshold
Herminiimonas fonticola	strain=S-94	GCA_003293745.1	303380	303380	type	True	78.5627	438	1009	95	below_threshold
Herminiimonas arsenitoxidans	strain=AS8	GCA_900130075.1	1809410	1809410	type	True	78.4857	386	1009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:20:08,007] [INFO] DFAST Taxonomy check result was written to GCF_014635845.1_ASM1463584v1_genomic.fna/tc_result.tsv
[2024-01-25 20:20:08,008] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:20:08,008] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:20:08,008] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0e6b005-b388-48a3-ae55-6d89083b6a34/dqc_reference/checkm_data
[2024-01-25 20:20:08,009] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:20:08,040] [INFO] Task started: CheckM
[2024-01-25 20:20:08,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635845.1_ASM1463584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635845.1_ASM1463584v1_genomic.fna/checkm_input GCF_014635845.1_ASM1463584v1_genomic.fna/checkm_result
[2024-01-25 20:20:37,055] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:37,057] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:37,081] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:37,081] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:37,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635845.1_ASM1463584v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:37,082] [INFO] Task started: Blastn
[2024-01-25 20:20:37,082] [INFO] Running command: blastn -query GCF_014635845.1_ASM1463584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0e6b005-b388-48a3-ae55-6d89083b6a34/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635845.1_ASM1463584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:38,980] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:38,983] [INFO] Selected 23 target genomes.
[2024-01-25 20:20:38,983] [INFO] Target genome list was writen to GCF_014635845.1_ASM1463584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:39,003] [INFO] Task started: fastANI
[2024-01-25 20:20:39,003] [INFO] Running command: fastANI --query /var/lib/cwl/stgda0afec9-78fd-4fce-bdc8-f60ffec2f540/GCF_014635845.1_ASM1463584v1_genomic.fna.gz --refList GCF_014635845.1_ASM1463584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635845.1_ASM1463584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:00,645] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:00,659] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:00,659] [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_014635845.1	s__Oxalicibacterium solurbis	100.0	1009	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014635065.1	s__Oxalicibacterium flavum	82.32	654	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	79.775	415	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744395.1	s__Herbaspirillum sp017744395	79.7643	428	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001189955.1	s__Herbaspirillum chlorophenolicum	79.5714	385	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	99.98	99.98	0.99	0.99	2	-
GCA_004134995.1	s__Herbaspirillum sp004134995	79.5464	396	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577615.1	s__Herbaspirillum sp000577615	79.5182	409	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009914615.1	s__Herbaspirillum frisingense_B	79.4958	410	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	79.4652	369	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004563925.1	s__Herbaspirillum sp004563925	79.3621	418	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	99.99	0.98	0.95	4	-
GCF_000818395.1	s__Noviherbaspirillum autotrophicum	79.2819	405	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584145.1	s__Collimonas fungivorans	79.2697	381	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000221045.1	s__Collimonas fungivorans_A	79.261	402	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCA_003537575.1	s__Paucimonas sp003537575	79.23	374	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211445.1	s__Noviherbaspirillum denitrificans	79.2121	400	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622895.1	s__AVCC01 sp000622895	79.1766	306	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AVCC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013625.1	s__Herminiimonas sp000013625	78.9829	486	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241865.1	s__Paucimonas sp018241865	78.9585	260	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112135.1	s__Collimonas sp900112135	78.9404	411	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	96.00	96.00	0.87	0.87	2	-
GCF_003852535.1	s__Herminiimonas sp003852535	78.8987	449	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herminiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804275.1	s__Noviherbaspirillum sp004804275	78.8801	371	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	78.8624	407	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376645.1	s__CAILRJ01 sp014376645	78.752	288	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:00,660] [INFO] GTDB search result was written to GCF_014635845.1_ASM1463584v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:00,661] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:00,678] [INFO] DFAST_QC result json was written to GCF_014635845.1_ASM1463584v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:00,679] [INFO] DFAST_QC completed!
[2024-01-25 20:21:00,679] [INFO] Total running time: 0h1m25s