[2024-01-24 14:38:47,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:47,016] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:47,016] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c761d2a-c6ec-44d4-b163-e5aa26a51a48/dqc_reference
[2024-01-24 14:38:48,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,452] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,453] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd3a0806-8081-413a-b926-5bdeecd55724/GCF_002890935.1_ASM289093v1_genomic.fna.gz | prodigal -d GCF_002890935.1_ASM289093v1_genomic.fna/cds.fna -a GCF_002890935.1_ASM289093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:02,314] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:02,314] [INFO] Task started: HMMsearch
[2024-01-24 14:39:02,314] [INFO] Running command: hmmsearch --tblout GCF_002890935.1_ASM289093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c761d2a-c6ec-44d4-b163-e5aa26a51a48/dqc_reference/reference_markers.hmm GCF_002890935.1_ASM289093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:02,620] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:02,622] [INFO] Found 6/6 markers.
[2024-01-24 14:39:02,663] [INFO] Query marker FASTA was written to GCF_002890935.1_ASM289093v1_genomic.fna/markers.fasta
[2024-01-24 14:39:02,663] [INFO] Task started: Blastn
[2024-01-24 14:39:02,663] [INFO] Running command: blastn -query GCF_002890935.1_ASM289093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c761d2a-c6ec-44d4-b163-e5aa26a51a48/dqc_reference/reference_markers.fasta -out GCF_002890935.1_ASM289093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:03,706] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:03,709] [INFO] Selected 9 target genomes.
[2024-01-24 14:39:03,710] [INFO] Target genome list was writen to GCF_002890935.1_ASM289093v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:03,713] [INFO] Task started: fastANI
[2024-01-24 14:39:03,714] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd3a0806-8081-413a-b926-5bdeecd55724/GCF_002890935.1_ASM289093v1_genomic.fna.gz --refList GCF_002890935.1_ASM289093v1_genomic.fna/target_genomes.txt --output GCF_002890935.1_ASM289093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:13,807] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:13,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c761d2a-c6ec-44d4-b163-e5aa26a51a48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:13,809] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c761d2a-c6ec-44d4-b163-e5aa26a51a48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:13,822] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:39:13,822] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:13,822] [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
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	100.0	1456	1457	95	conclusive
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	99.9999	1456	1457	95	conclusive
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	99.988	1439	1457	95	conclusive
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	91.2094	1255	1457	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	91.168	1258	1457	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	88.7257	1215	1457	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	88.6458	1182	1457	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	88.6455	1191	1457	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	88.6342	1203	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:13,824] [INFO] DFAST Taxonomy check result was written to GCF_002890935.1_ASM289093v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:13,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:13,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:13,824] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c761d2a-c6ec-44d4-b163-e5aa26a51a48/dqc_reference/checkm_data
[2024-01-24 14:39:13,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:13,871] [INFO] Task started: CheckM
[2024-01-24 14:39:13,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002890935.1_ASM289093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002890935.1_ASM289093v1_genomic.fna/checkm_input GCF_002890935.1_ASM289093v1_genomic.fna/checkm_result
[2024-01-24 14:39:55,440] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:55,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:55,461] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:55,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:55,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002890935.1_ASM289093v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:55,462] [INFO] Task started: Blastn
[2024-01-24 14:39:55,462] [INFO] Running command: blastn -query GCF_002890935.1_ASM289093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c761d2a-c6ec-44d4-b163-e5aa26a51a48/dqc_reference/reference_markers_gtdb.fasta -out GCF_002890935.1_ASM289093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:57,656] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:57,661] [INFO] Selected 17 target genomes.
[2024-01-24 14:39:57,661] [INFO] Target genome list was writen to GCF_002890935.1_ASM289093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:57,674] [INFO] Task started: fastANI
[2024-01-24 14:39:57,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd3a0806-8081-413a-b926-5bdeecd55724/GCF_002890935.1_ASM289093v1_genomic.fna.gz --refList GCF_002890935.1_ASM289093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002890935.1_ASM289093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:18,013] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:18,028] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:18,028] [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_003205815.1	s__Pseudomonas_A sp003205815	96.9727	1331	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	conclusive
GCF_000219605.1	s__Pseudomonas_A stutzeri	91.1767	1257	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_014764705.1	s__Pseudomonas_A sp002692525	88.9942	1211	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0332	98.20	97.14	0.91	0.83	13	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	88.9632	1230	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_000341615.1	s__Pseudomonas_A stutzeri_G	88.9489	1213	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.57	97.27	0.90	0.83	4	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	88.7612	1243	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0636	N/A	N/A	N/A	N/A	1	-
GCF_002929225.1	s__Pseudomonas_A stutzeri_U	88.7527	1244	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0711	97.19	97.19	0.89	0.89	2	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	88.6537	1190	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCA_003488145.1	s__Pseudomonas_A sp003488145	88.0521	799	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.7169	97.61	97.61	0.74	0.74	2	-
GCF_000661915.1	s__Pseudomonas_A stutzeri_A	87.8852	1232	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.44	99.44	0.92	0.92	2	-
GCF_000327065.1	s__Pseudomonas_A stutzeri_AE	87.8803	1256	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	87.0696	1151	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_015291885.1	s__Pseudomonas_A stutzeri_AC	86.89	1193	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.94	97.56	0.91	0.88	14	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	86.8179	1157	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_002890795.1	s__Pseudomonas_A stutzeri_AA	86.0557	1195	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	85.7992	1089	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_907163115.1	s__Pseudomonas_A stutzeri_AL	85.0332	1039	1457	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.05	96.55	0.94	0.91	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:18,037] [INFO] GTDB search result was written to GCF_002890935.1_ASM289093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:18,038] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:18,041] [INFO] DFAST_QC result json was written to GCF_002890935.1_ASM289093v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:18,042] [INFO] DFAST_QC completed!
[2024-01-24 14:40:18,042] [INFO] Total running time: 0h1m31s