[2024-01-24 11:44:22,864] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:22,868] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:22,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a150f6a-34fa-4aa6-afca-3e2ba6c0e3c5/dqc_reference
[2024-01-24 11:44:26,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,349] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,349] [INFO] Running command: gunzip -c /var/lib/cwl/stg72da95c4-85f7-43c4-b6a0-4fef82253c27/GCF_025146415.1_ASM2514641v1_genomic.fna.gz | prodigal -d GCF_025146415.1_ASM2514641v1_genomic.fna/cds.fna -a GCF_025146415.1_ASM2514641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:54,985] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:54,986] [INFO] Task started: HMMsearch
[2024-01-24 11:44:54,986] [INFO] Running command: hmmsearch --tblout GCF_025146415.1_ASM2514641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a150f6a-34fa-4aa6-afca-3e2ba6c0e3c5/dqc_reference/reference_markers.hmm GCF_025146415.1_ASM2514641v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:55,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:55,298] [INFO] Found 6/6 markers.
[2024-01-24 11:44:55,342] [INFO] Query marker FASTA was written to GCF_025146415.1_ASM2514641v1_genomic.fna/markers.fasta
[2024-01-24 11:44:55,343] [INFO] Task started: Blastn
[2024-01-24 11:44:55,343] [INFO] Running command: blastn -query GCF_025146415.1_ASM2514641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a150f6a-34fa-4aa6-afca-3e2ba6c0e3c5/dqc_reference/reference_markers.fasta -out GCF_025146415.1_ASM2514641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:55,984] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:55,988] [INFO] Selected 9 target genomes.
[2024-01-24 11:44:55,988] [INFO] Target genome list was writen to GCF_025146415.1_ASM2514641v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:55,993] [INFO] Task started: fastANI
[2024-01-24 11:44:55,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg72da95c4-85f7-43c4-b6a0-4fef82253c27/GCF_025146415.1_ASM2514641v1_genomic.fna.gz --refList GCF_025146415.1_ASM2514641v1_genomic.fna/target_genomes.txt --output GCF_025146415.1_ASM2514641v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:06,753] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:06,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a150f6a-34fa-4aa6-afca-3e2ba6c0e3c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:06,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a150f6a-34fa-4aa6-afca-3e2ba6c0e3c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:06,768] [INFO] Found 9 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:45:06,768] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:45:06,768] [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_025146415.1	357276	357276	type	True	100.0	1869	1875	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	99.9947	1861	1875	95	inconclusive
Phocaeicola dorei	strain=DSM 17855	GCA_000156075.1	357276	357276	type	True	99.9189	1829	1875	95	inconclusive
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	95.2992	1315	1875	95	inconclusive
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	95.2842	1316	1875	95	inconclusive
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	89.877	1147	1875	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	81.7419	230	1875	95	below_threshold
Phocaeicola faecalis	strain=FXJYN30E22	GCA_021730445.1	2786956	2786956	type	True	81.5626	610	1875	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.5118	253	1875	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:06,770] [INFO] DFAST Taxonomy check result was written to GCF_025146415.1_ASM2514641v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:06,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:06,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:06,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a150f6a-34fa-4aa6-afca-3e2ba6c0e3c5/dqc_reference/checkm_data
[2024-01-24 11:45:06,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:06,824] [INFO] Task started: CheckM
[2024-01-24 11:45:06,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025146415.1_ASM2514641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025146415.1_ASM2514641v1_genomic.fna/checkm_input GCF_025146415.1_ASM2514641v1_genomic.fna/checkm_result
[2024-01-24 11:46:24,475] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:24,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:24,496] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:24,497] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:24,497] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025146415.1_ASM2514641v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:24,497] [INFO] Task started: Blastn
[2024-01-24 11:46:24,498] [INFO] Running command: blastn -query GCF_025146415.1_ASM2514641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a150f6a-34fa-4aa6-afca-3e2ba6c0e3c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_025146415.1_ASM2514641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:25,355] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:25,360] [INFO] Selected 8 target genomes.
[2024-01-24 11:46:25,360] [INFO] Target genome list was writen to GCF_025146415.1_ASM2514641v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:25,367] [INFO] Task started: fastANI
[2024-01-24 11:46:25,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg72da95c4-85f7-43c4-b6a0-4fef82253c27/GCF_025146415.1_ASM2514641v1_genomic.fna.gz --refList GCF_025146415.1_ASM2514641v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025146415.1_ASM2514641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:34,816] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:34,836] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:34,837] [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	99.9948	1860	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	95.2528	1319	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	90.8842	794	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	89.8735	1145	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	89.5917	831	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	81.9128	647	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	81.4656	839	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	80.2652	516	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 11:46:34,839] [INFO] GTDB search result was written to GCF_025146415.1_ASM2514641v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:34,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:34,843] [INFO] DFAST_QC result json was written to GCF_025146415.1_ASM2514641v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:34,843] [INFO] DFAST_QC completed!
[2024-01-24 11:46:34,844] [INFO] Total running time: 0h2m12s