[2024-01-24 13:28:19,030] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:19,034] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:19,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f1eda3f-979f-425f-9788-5da99313eb05/dqc_reference
[2024-01-24 13:28:20,393] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:20,394] [INFO] Task started: Prodigal
[2024-01-24 13:28:20,394] [INFO] Running command: gunzip -c /var/lib/cwl/stg1972ebb4-591a-4b15-97c5-5dafb5ac6706/GCF_021166475.1_ASM2116647v1_genomic.fna.gz | prodigal -d GCF_021166475.1_ASM2116647v1_genomic.fna/cds.fna -a GCF_021166475.1_ASM2116647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:30,977] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:30,977] [INFO] Task started: HMMsearch
[2024-01-24 13:28:30,977] [INFO] Running command: hmmsearch --tblout GCF_021166475.1_ASM2116647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f1eda3f-979f-425f-9788-5da99313eb05/dqc_reference/reference_markers.hmm GCF_021166475.1_ASM2116647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:31,256] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:31,258] [INFO] Found 6/6 markers.
[2024-01-24 13:28:31,288] [INFO] Query marker FASTA was written to GCF_021166475.1_ASM2116647v1_genomic.fna/markers.fasta
[2024-01-24 13:28:31,289] [INFO] Task started: Blastn
[2024-01-24 13:28:31,289] [INFO] Running command: blastn -query GCF_021166475.1_ASM2116647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f1eda3f-979f-425f-9788-5da99313eb05/dqc_reference/reference_markers.fasta -out GCF_021166475.1_ASM2116647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:32,258] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:32,261] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:32,262] [INFO] Target genome list was writen to GCF_021166475.1_ASM2116647v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:32,270] [INFO] Task started: fastANI
[2024-01-24 13:28:32,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg1972ebb4-591a-4b15-97c5-5dafb5ac6706/GCF_021166475.1_ASM2116647v1_genomic.fna.gz --refList GCF_021166475.1_ASM2116647v1_genomic.fna/target_genomes.txt --output GCF_021166475.1_ASM2116647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:43,348] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:43,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f1eda3f-979f-425f-9788-5da99313eb05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:43,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f1eda3f-979f-425f-9788-5da99313eb05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:43,361] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:43,362] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:43,362] [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
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	100.0	1118	1119	95	conclusive
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	79.2598	442	1119	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	79.1794	426	1119	95	below_threshold
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	79.0846	456	1119	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	78.8028	412	1119	95	below_threshold
Pelagibacterium limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	78.5332	411	1119	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	78.4241	414	1119	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	77.5141	227	1119	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.4644	261	1119	95	below_threshold
Devosia subaequoris	strain=DSM 23447	GCA_014197055.1	395930	395930	type	True	77.41	230	1119	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	77.4008	304	1119	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	77.2518	217	1119	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	76.7608	134	1119	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	76.705	145	1119	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.615	97	1119	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:43,364] [INFO] DFAST Taxonomy check result was written to GCF_021166475.1_ASM2116647v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:43,364] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:43,365] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:43,365] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f1eda3f-979f-425f-9788-5da99313eb05/dqc_reference/checkm_data
[2024-01-24 13:28:43,366] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:43,401] [INFO] Task started: CheckM
[2024-01-24 13:28:43,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021166475.1_ASM2116647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021166475.1_ASM2116647v1_genomic.fna/checkm_input GCF_021166475.1_ASM2116647v1_genomic.fna/checkm_result
[2024-01-24 13:29:16,633] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:16,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:16,655] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:16,656] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:16,656] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021166475.1_ASM2116647v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:16,657] [INFO] Task started: Blastn
[2024-01-24 13:29:16,657] [INFO] Running command: blastn -query GCF_021166475.1_ASM2116647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f1eda3f-979f-425f-9788-5da99313eb05/dqc_reference/reference_markers_gtdb.fasta -out GCF_021166475.1_ASM2116647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:18,422] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:18,426] [INFO] Selected 16 target genomes.
[2024-01-24 13:29:18,426] [INFO] Target genome list was writen to GCF_021166475.1_ASM2116647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:18,440] [INFO] Task started: fastANI
[2024-01-24 13:29:18,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg1972ebb4-591a-4b15-97c5-5dafb5ac6706/GCF_021166475.1_ASM2116647v1_genomic.fna.gz --refList GCF_021166475.1_ASM2116647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021166475.1_ASM2116647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:28,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:28,950] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:29:28,950] [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_003345525.1	s__Pelagibacterium lacus	79.2598	442	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390885.1	s__Pelagibacterium sp003390885	79.1906	425	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230555.1	s__Pelagibacterium halotolerans	79.0846	456	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002337455.1	s__Pelagibacterium sp002337455	78.8788	440	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCF_003992665.1	s__Pelagibacterium montanilacus	78.7983	413	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002375765.1	s__Pelagibacterium sp002375765	78.7864	433	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCA_002723255.1	s__Pelagibacterium sp002723255	78.72	379	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCF_015694405.1	s__Pelagibacterium limicola	78.5105	414	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100665.1	s__Pelagibacterium luteolum	78.4241	414	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014837245.1	s__Devosia sp014837245	77.4859	238	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698645.1	s__Devosia sp016698645	77.4563	261	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698665.1	s__Devosia sp016698665	77.2651	216	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470445.1	s__Devosia sp900470445	77.224	254	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
GCA_015234425.1	s__Devosia sp015234425	77.1801	232	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043005.1	s__Martelella mediterranea	76.8295	187	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	-
GCA_003241695.1	s__Hansschlegelia sp003241695	76.2384	136	1119	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:28,952] [INFO] GTDB search result was written to GCF_021166475.1_ASM2116647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:28,952] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:28,956] [INFO] DFAST_QC result json was written to GCF_021166475.1_ASM2116647v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:28,956] [INFO] DFAST_QC completed!
[2024-01-24 13:29:28,956] [INFO] Total running time: 0h1m10s