[2024-01-24 14:22:01,873] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:01,874] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:01,874] [INFO] DQC Reference Directory: /var/lib/cwl/stg0acb6da0-d681-4521-ad33-adda897d5a0c/dqc_reference
[2024-01-24 14:22:03,092] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:03,093] [INFO] Task started: Prodigal
[2024-01-24 14:22:03,093] [INFO] Running command: gunzip -c /var/lib/cwl/stg8331f75a-365a-49fd-86cd-d70d9fbaa24a/GCF_014837065.1_ASM1483706v1_genomic.fna.gz | prodigal -d GCF_014837065.1_ASM1483706v1_genomic.fna/cds.fna -a GCF_014837065.1_ASM1483706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:26,334] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:26,334] [INFO] Task started: HMMsearch
[2024-01-24 14:22:26,334] [INFO] Running command: hmmsearch --tblout GCF_014837065.1_ASM1483706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0acb6da0-d681-4521-ad33-adda897d5a0c/dqc_reference/reference_markers.hmm GCF_014837065.1_ASM1483706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:26,625] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:26,627] [INFO] Found 6/6 markers.
[2024-01-24 14:22:26,661] [INFO] Query marker FASTA was written to GCF_014837065.1_ASM1483706v1_genomic.fna/markers.fasta
[2024-01-24 14:22:26,661] [INFO] Task started: Blastn
[2024-01-24 14:22:26,661] [INFO] Running command: blastn -query GCF_014837065.1_ASM1483706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0acb6da0-d681-4521-ad33-adda897d5a0c/dqc_reference/reference_markers.fasta -out GCF_014837065.1_ASM1483706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:27,343] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:27,346] [INFO] Selected 21 target genomes.
[2024-01-24 14:22:27,347] [INFO] Target genome list was writen to GCF_014837065.1_ASM1483706v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:27,357] [INFO] Task started: fastANI
[2024-01-24 14:22:27,357] [INFO] Running command: fastANI --query /var/lib/cwl/stg8331f75a-365a-49fd-86cd-d70d9fbaa24a/GCF_014837065.1_ASM1483706v1_genomic.fna.gz --refList GCF_014837065.1_ASM1483706v1_genomic.fna/target_genomes.txt --output GCF_014837065.1_ASM1483706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:44,228] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:44,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0acb6da0-d681-4521-ad33-adda897d5a0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:44,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0acb6da0-d681-4521-ad33-adda897d5a0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:44,245] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:44,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:44,245] [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 intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	100.0	1278	1284	95	conclusive
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	88.5535	705	1284	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	80.2761	294	1284	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	80.1231	288	1284	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	79.2445	141	1284	95	below_threshold
Bacteroides fluxus	strain=YIT 12057	GCA_000195635.1	626930	626930	type	True	79.0258	132	1284	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	78.9728	147	1284	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	78.8992	264	1284	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	78.767	274	1284	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	78.5738	259	1284	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.3385	215	1284	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.3288	209	1284	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	77.8726	161	1284	95	below_threshold
Phocaeicola vulgatus	strain=FDAARGOS_1098	GCA_016766915.1	821	821	type	True	77.4219	159	1284	95	below_threshold
Phocaeicola vulgatus	strain=ATCC 8482	GCA_000012825.1	821	821	type	True	77.4103	155	1284	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	77.1916	94	1284	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	77.1902	102	1284	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	77.1597	99	1284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:44,247] [INFO] DFAST Taxonomy check result was written to GCF_014837065.1_ASM1483706v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:44,248] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:44,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:44,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0acb6da0-d681-4521-ad33-adda897d5a0c/dqc_reference/checkm_data
[2024-01-24 14:22:44,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:44,292] [INFO] Task started: CheckM
[2024-01-24 14:22:44,292] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837065.1_ASM1483706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837065.1_ASM1483706v1_genomic.fna/checkm_input GCF_014837065.1_ASM1483706v1_genomic.fna/checkm_result
[2024-01-24 14:23:44,592] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:44,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:44,611] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:44,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:44,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837065.1_ASM1483706v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:44,612] [INFO] Task started: Blastn
[2024-01-24 14:23:44,612] [INFO] Running command: blastn -query GCF_014837065.1_ASM1483706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0acb6da0-d681-4521-ad33-adda897d5a0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837065.1_ASM1483706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:45,468] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:45,472] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:45,472] [INFO] Target genome list was writen to GCF_014837065.1_ASM1483706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:45,483] [INFO] Task started: fastANI
[2024-01-24 14:23:45,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg8331f75a-365a-49fd-86cd-d70d9fbaa24a/GCF_014837065.1_ASM1483706v1_genomic.fna.gz --refList GCF_014837065.1_ASM1483706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837065.1_ASM1483706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:54,990] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:55,001] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:55,001] [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_016899805.1	s__Phocaeicola gallinaceus	98.2011	1003	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.20	97.80	0.80	0.74	12	conclusive
GCF_000190575.1	s__Phocaeicola salanitronis	88.5721	704	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.68	97.68	0.88	0.88	2	-
GCA_900546355.1	s__Phocaeicola sp900546355	85.5251	589	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	100.00	100.00	0.98	0.98	2	-
GCF_002161765.1	s__Phocaeicola merdavium	81.9375	598	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	98.22	0.87	0.86	5	-
GCA_900544675.1	s__Phocaeicola sp900544675	81.2892	655	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.98	99.96	0.94	0.90	3	-
GCF_016901995.1	s__Phocaeicola sp900066445	80.8055	169	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.12	97.12	0.79	0.79	3	-
GCF_000374585.1	s__Phocaeicola barnesiae	80.2633	294	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCF_016900355.1	s__Phocaeicola sp900551065	78.9271	264	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	96.34	95.04	0.86	0.84	4	-
GCF_000154845.1	s__Phocaeicola coprocola	78.7115	276	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCA_019116045.1	s__Bacteroides merdipullorum	77.5853	116	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000436795.1	s__Phocaeicola sp000436795	77.4308	204	1284	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:55,003] [INFO] GTDB search result was written to GCF_014837065.1_ASM1483706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:55,004] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:55,008] [INFO] DFAST_QC result json was written to GCF_014837065.1_ASM1483706v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:55,008] [INFO] DFAST_QC completed!
[2024-01-24 14:23:55,008] [INFO] Total running time: 0h1m53s