[2024-01-24 11:34:37,296] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:37,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:37,298] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7e9015b-11c4-4a3b-ab81-143f49e235b2/dqc_reference
[2024-01-24 11:34:39,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:39,642] [INFO] Task started: Prodigal
[2024-01-24 11:34:39,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg588051ca-15a6-44f3-a851-585e0e63914f/GCF_016028515.1_ASM1602851v1_genomic.fna.gz | prodigal -d GCF_016028515.1_ASM1602851v1_genomic.fna/cds.fna -a GCF_016028515.1_ASM1602851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:52,859] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:52,859] [INFO] Task started: HMMsearch
[2024-01-24 11:34:52,859] [INFO] Running command: hmmsearch --tblout GCF_016028515.1_ASM1602851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7e9015b-11c4-4a3b-ab81-143f49e235b2/dqc_reference/reference_markers.hmm GCF_016028515.1_ASM1602851v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,173] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,174] [INFO] Found 6/6 markers.
[2024-01-24 11:34:53,213] [INFO] Query marker FASTA was written to GCF_016028515.1_ASM1602851v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,213] [INFO] Task started: Blastn
[2024-01-24 11:34:53,213] [INFO] Running command: blastn -query GCF_016028515.1_ASM1602851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7e9015b-11c4-4a3b-ab81-143f49e235b2/dqc_reference/reference_markers.fasta -out GCF_016028515.1_ASM1602851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:54,293] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:54,297] [INFO] Selected 9 target genomes.
[2024-01-24 11:34:54,297] [INFO] Target genome list was writen to GCF_016028515.1_ASM1602851v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:54,300] [INFO] Task started: fastANI
[2024-01-24 11:34:54,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg588051ca-15a6-44f3-a851-585e0e63914f/GCF_016028515.1_ASM1602851v1_genomic.fna.gz --refList GCF_016028515.1_ASM1602851v1_genomic.fna/target_genomes.txt --output GCF_016028515.1_ASM1602851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:04,472] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:04,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7e9015b-11c4-4a3b-ab81-143f49e235b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:04,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7e9015b-11c4-4a3b-ab81-143f49e235b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:04,481] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:35:04,482] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:04,482] [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=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	100.0	1464	1464	95	conclusive
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	99.9977	1455	1464	95	conclusive
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	99.9794	1443	1464	95	conclusive
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	91.3281	1243	1464	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	91.2107	1258	1464	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	88.6752	1230	1464	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	88.6403	1183	1464	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	88.5037	1194	1464	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	88.4468	1202	1464	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:04,483] [INFO] DFAST Taxonomy check result was written to GCF_016028515.1_ASM1602851v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:04,484] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:04,484] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:04,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7e9015b-11c4-4a3b-ab81-143f49e235b2/dqc_reference/checkm_data
[2024-01-24 11:35:04,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:04,527] [INFO] Task started: CheckM
[2024-01-24 11:35:04,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016028515.1_ASM1602851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016028515.1_ASM1602851v1_genomic.fna/checkm_input GCF_016028515.1_ASM1602851v1_genomic.fna/checkm_result
[2024-01-24 11:35:45,607] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:45,609] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:45,625] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:45,626] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:45,626] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016028515.1_ASM1602851v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:45,626] [INFO] Task started: Blastn
[2024-01-24 11:35:45,627] [INFO] Running command: blastn -query GCF_016028515.1_ASM1602851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7e9015b-11c4-4a3b-ab81-143f49e235b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016028515.1_ASM1602851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:47,521] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:47,524] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:47,524] [INFO] Target genome list was writen to GCF_016028515.1_ASM1602851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:47,547] [INFO] Task started: fastANI
[2024-01-24 11:35:47,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg588051ca-15a6-44f3-a851-585e0e63914f/GCF_016028515.1_ASM1602851v1_genomic.fna.gz --refList GCF_016028515.1_ASM1602851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016028515.1_ASM1602851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:05,235] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:05,249] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:05,250] [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	97.0323	1330	1464	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	91.3121	1243	1464	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	89.0446	1217	1464	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_000341615.1	s__Pseudomonas_A stutzeri_G	88.9836	1204	1464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.57	97.27	0.90	0.83	4	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	88.9189	1261	1464	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	88.7585	1245	1464	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	88.695	1268	1464	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	88.5031	1193	1464	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	88.0288	803	1464	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	87.9714	1248	1464	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	87.9238	1246	1464	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	87.0498	1143	1464	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	87.0153	1186	1464	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	86.9521	1139	1464	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	86.0896	1207	1464	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	85.9642	1067	1464	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	85.0578	1040	1464	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 11:36:05,251] [INFO] GTDB search result was written to GCF_016028515.1_ASM1602851v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:05,252] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:05,255] [INFO] DFAST_QC result json was written to GCF_016028515.1_ASM1602851v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:05,255] [INFO] DFAST_QC completed!
[2024-01-24 11:36:05,255] [INFO] Total running time: 0h1m28s