[2024-01-24 13:28:11,215] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:11,221] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:11,221] [INFO] DQC Reference Directory: /var/lib/cwl/stg20c62ad9-05dd-41a8-b642-8fefd5a134b3/dqc_reference
[2024-01-24 13:28:12,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:12,486] [INFO] Task started: Prodigal
[2024-01-24 13:28:12,486] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf674e94-d147-46f7-b85e-92a316e771b8/GCF_013009555.1_ASM1300955v1_genomic.fna.gz | prodigal -d GCF_013009555.1_ASM1300955v1_genomic.fna/cds.fna -a GCF_013009555.1_ASM1300955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:41,066] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:41,066] [INFO] Task started: HMMsearch
[2024-01-24 13:28:41,066] [INFO] Running command: hmmsearch --tblout GCF_013009555.1_ASM1300955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20c62ad9-05dd-41a8-b642-8fefd5a134b3/dqc_reference/reference_markers.hmm GCF_013009555.1_ASM1300955v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:41,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:41,374] [INFO] Found 6/6 markers.
[2024-01-24 13:28:41,419] [INFO] Query marker FASTA was written to GCF_013009555.1_ASM1300955v1_genomic.fna/markers.fasta
[2024-01-24 13:28:41,419] [INFO] Task started: Blastn
[2024-01-24 13:28:41,419] [INFO] Running command: blastn -query GCF_013009555.1_ASM1300955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c62ad9-05dd-41a8-b642-8fefd5a134b3/dqc_reference/reference_markers.fasta -out GCF_013009555.1_ASM1300955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,039] [INFO] Selected 9 target genomes.
[2024-01-24 13:28:42,039] [INFO] Target genome list was writen to GCF_013009555.1_ASM1300955v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:42,319] [INFO] Task started: fastANI
[2024-01-24 13:28:42,319] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf674e94-d147-46f7-b85e-92a316e771b8/GCF_013009555.1_ASM1300955v1_genomic.fna.gz --refList GCF_013009555.1_ASM1300955v1_genomic.fna/target_genomes.txt --output GCF_013009555.1_ASM1300955v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:52,867] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:52,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20c62ad9-05dd-41a8-b642-8fefd5a134b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:52,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20c62ad9-05dd-41a8-b642-8fefd5a134b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:52,886] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:28:52,886] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:28:52,886] [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
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	100.0	1868	1875	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	99.9903	1866	1875	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_000156075.1	357276	357276	type	True	99.9204	1831	1875	95	inconclusive
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	95.227	1323	1875	95	inconclusive
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	95.223	1321	1875	95	inconclusive
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	89.7875	1152	1875	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	81.7699	223	1875	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	81.3498	633	1875	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.6218	247	1875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:52,888] [INFO] DFAST Taxonomy check result was written to GCF_013009555.1_ASM1300955v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:52,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:52,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:52,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20c62ad9-05dd-41a8-b642-8fefd5a134b3/dqc_reference/checkm_data
[2024-01-24 13:28:52,891] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:52,942] [INFO] Task started: CheckM
[2024-01-24 13:28:52,942] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013009555.1_ASM1300955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013009555.1_ASM1300955v1_genomic.fna/checkm_input GCF_013009555.1_ASM1300955v1_genomic.fna/checkm_result
[2024-01-24 13:30:11,077] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:11,078] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:11,100] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:11,101] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:11,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013009555.1_ASM1300955v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:11,102] [INFO] Task started: Blastn
[2024-01-24 13:30:11,102] [INFO] Running command: blastn -query GCF_013009555.1_ASM1300955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg20c62ad9-05dd-41a8-b642-8fefd5a134b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_013009555.1_ASM1300955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:11,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:11,979] [INFO] Selected 8 target genomes.
[2024-01-24 13:30:11,980] [INFO] Target genome list was writen to GCF_013009555.1_ASM1300955v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:12,009] [INFO] Task started: fastANI
[2024-01-24 13:30:12,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf674e94-d147-46f7-b85e-92a316e771b8/GCF_013009555.1_ASM1300955v1_genomic.fna.gz --refList GCF_013009555.1_ASM1300955v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013009555.1_ASM1300955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:21,017] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:21,033] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:21,033] [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_013009555.1	s__Phocaeicola dorei	100.0	1869	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	99.04	97.27	0.84	0.54	104	conclusive
GCF_000012825.1	s__Phocaeicola vulgatus	95.2132	1324	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.359	98.84	95.43	0.81	0.61	263	-
GCA_900760795.1	s__Phocaeicola sp900760795	91.0245	787	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614185.1	s__Phocaeicola sartorii	89.8173	1133	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.95	98.44	0.85	0.76	7	-
GCA_011959205.1	s__Phocaeicola sp011959205	89.5659	841	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.90	0.90	2	-
GCF_000382445.1	s__Phocaeicola massiliensis	82.049	630	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.84	98.03	0.86	0.62	25	-
GCA_902388365.1	s__Phocaeicola sp902388365	81.4378	850	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.75	97.52	0.90	0.83	3	-
GCA_002493165.1	s__Phocaeicola sp002493165	80.1623	527	1875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.20	98.75	0.86	0.83	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:21,035] [INFO] GTDB search result was written to GCF_013009555.1_ASM1300955v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:21,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:21,041] [INFO] DFAST_QC result json was written to GCF_013009555.1_ASM1300955v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:21,041] [INFO] DFAST_QC completed!
[2024-01-24 13:30:21,041] [INFO] Total running time: 0h2m10s