[2024-01-24 12:44:43,776] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,778] [INFO] DQC Reference Directory: /var/lib/cwl/stgd7a48cc3-30b8-49fe-a85a-dbc391fdf30c/dqc_reference
[2024-01-24 12:44:45,178] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,179] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,179] [INFO] Running command: gunzip -c /var/lib/cwl/stgd40fef7d-35e4-4f54-99d1-2fa30d23c7a7/GCF_025567135.1_ASM2556713v1_genomic.fna.gz | prodigal -d GCF_025567135.1_ASM2556713v1_genomic.fna/cds.fna -a GCF_025567135.1_ASM2556713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:02,506] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:02,507] [INFO] Task started: HMMsearch
[2024-01-24 12:45:02,507] [INFO] Running command: hmmsearch --tblout GCF_025567135.1_ASM2556713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd7a48cc3-30b8-49fe-a85a-dbc391fdf30c/dqc_reference/reference_markers.hmm GCF_025567135.1_ASM2556713v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:02,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:02,813] [INFO] Found 6/6 markers.
[2024-01-24 12:45:02,852] [INFO] Query marker FASTA was written to GCF_025567135.1_ASM2556713v1_genomic.fna/markers.fasta
[2024-01-24 12:45:02,852] [INFO] Task started: Blastn
[2024-01-24 12:45:02,852] [INFO] Running command: blastn -query GCF_025567135.1_ASM2556713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7a48cc3-30b8-49fe-a85a-dbc391fdf30c/dqc_reference/reference_markers.fasta -out GCF_025567135.1_ASM2556713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:03,484] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:03,488] [INFO] Selected 19 target genomes.
[2024-01-24 12:45:03,488] [INFO] Target genome list was writen to GCF_025567135.1_ASM2556713v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:03,499] [INFO] Task started: fastANI
[2024-01-24 12:45:03,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgd40fef7d-35e4-4f54-99d1-2fa30d23c7a7/GCF_025567135.1_ASM2556713v1_genomic.fna.gz --refList GCF_025567135.1_ASM2556713v1_genomic.fna/target_genomes.txt --output GCF_025567135.1_ASM2556713v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:16,072] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:16,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd7a48cc3-30b8-49fe-a85a-dbc391fdf30c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:16,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd7a48cc3-30b8-49fe-a85a-dbc391fdf30c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:16,087] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:16,088] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:16,088] [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 faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	80.639	253	1180	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	80.4816	241	1180	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	80.4466	240	1180	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	79.4239	174	1180	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_013009555.1	357276	357276	type	True	79.3063	165	1180	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	79.1658	274	1180	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	78.9223	267	1180	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	78.9116	140	1180	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.8929	244	1180	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.8429	248	1180	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_900106755.1	674529	674529	type	True	77.7752	119	1180	95	below_threshold
Bacteroides graminisolvens	strain=JCM 15093	GCA_000613825.1	477666	477666	type	True	77.5212	58	1180	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	77.4846	116	1180	95	below_threshold
Bacteroides graminisolvens	strain=DSM 19988	GCA_000428125.1	477666	477666	type	True	77.3061	60	1180	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:16,091] [INFO] DFAST Taxonomy check result was written to GCF_025567135.1_ASM2556713v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:16,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:16,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:16,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd7a48cc3-30b8-49fe-a85a-dbc391fdf30c/dqc_reference/checkm_data
[2024-01-24 12:45:16,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:16,145] [INFO] Task started: CheckM
[2024-01-24 12:45:16,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567135.1_ASM2556713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567135.1_ASM2556713v1_genomic.fna/checkm_input GCF_025567135.1_ASM2556713v1_genomic.fna/checkm_result
[2024-01-24 12:46:06,396] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:06,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:06,420] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:06,420] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:06,421] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567135.1_ASM2556713v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:06,421] [INFO] Task started: Blastn
[2024-01-24 12:46:06,421] [INFO] Running command: blastn -query GCF_025567135.1_ASM2556713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd7a48cc3-30b8-49fe-a85a-dbc391fdf30c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567135.1_ASM2556713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:07,292] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:07,296] [INFO] Selected 7 target genomes.
[2024-01-24 12:46:07,297] [INFO] Target genome list was writen to GCF_025567135.1_ASM2556713v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:07,331] [INFO] Task started: fastANI
[2024-01-24 12:46:07,331] [INFO] Running command: fastANI --query /var/lib/cwl/stgd40fef7d-35e4-4f54-99d1-2fa30d23c7a7/GCF_025567135.1_ASM2556713v1_genomic.fna.gz --refList GCF_025567135.1_ASM2556713v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567135.1_ASM2556713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:12,799] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:12,806] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:12,807] [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_016901995.1	s__Phocaeicola sp900066445	97.0988	917	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.12	97.12	0.79	0.79	3	conclusive
GCA_018883555.1	s__Phocaeicola faecigallinarum	89.7287	726	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016902295.1	s__Phocaeicola caecigallinarum_A	87.8124	734	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.48	97.48	0.83	0.83	2	-
GCA_900544075.1	s__Phocaeicola sp900544075	86.2552	656	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018884025.1	s__Phocaeicola faecipullorum_A	86.0749	604	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.13	97.13	0.68	0.68	2	-
GCA_000434735.1	s__Phocaeicola sp000434735	78.0732	196	1180	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.56	97.52	0.82	0.81	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:12,809] [INFO] GTDB search result was written to GCF_025567135.1_ASM2556713v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:12,809] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:12,812] [INFO] DFAST_QC result json was written to GCF_025567135.1_ASM2556713v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:12,812] [INFO] DFAST_QC completed!
[2024-01-24 12:46:12,813] [INFO] Total running time: 0h1m29s