[2024-01-24 13:27:40,937] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:40,939] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:40,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg83fd30d6-2434-4e7d-b44f-af0a129aefae/dqc_reference
[2024-01-24 13:27:42,158] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:42,159] [INFO] Task started: Prodigal
[2024-01-24 13:27:42,159] [INFO] Running command: gunzip -c /var/lib/cwl/stgc29c5bbd-9abb-4582-92ec-2e799e82140d/GCF_000614145.1_ASM61414v1_genomic.fna.gz | prodigal -d GCF_000614145.1_ASM61414v1_genomic.fna/cds.fna -a GCF_000614145.1_ASM61414v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:02,511] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:02,512] [INFO] Task started: HMMsearch
[2024-01-24 13:28:02,512] [INFO] Running command: hmmsearch --tblout GCF_000614145.1_ASM61414v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83fd30d6-2434-4e7d-b44f-af0a129aefae/dqc_reference/reference_markers.hmm GCF_000614145.1_ASM61414v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:02,809] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:02,811] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc29c5bbd-9abb-4582-92ec-2e799e82140d/GCF_000614145.1_ASM61414v1_genomic.fna.gz]
[2024-01-24 13:28:02,850] [INFO] Query marker FASTA was written to GCF_000614145.1_ASM61414v1_genomic.fna/markers.fasta
[2024-01-24 13:28:02,850] [INFO] Task started: Blastn
[2024-01-24 13:28:02,851] [INFO] Running command: blastn -query GCF_000614145.1_ASM61414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83fd30d6-2434-4e7d-b44f-af0a129aefae/dqc_reference/reference_markers.fasta -out GCF_000614145.1_ASM61414v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:03,500] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:03,504] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:03,504] [INFO] Target genome list was writen to GCF_000614145.1_ASM61414v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:03,560] [INFO] Task started: fastANI
[2024-01-24 13:28:03,560] [INFO] Running command: fastANI --query /var/lib/cwl/stgc29c5bbd-9abb-4582-92ec-2e799e82140d/GCF_000614145.1_ASM61414v1_genomic.fna.gz --refList GCF_000614145.1_ASM61414v1_genomic.fna/target_genomes.txt --output GCF_000614145.1_ASM61414v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:16,415] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:16,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83fd30d6-2434-4e7d-b44f-af0a129aefae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:16,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83fd30d6-2434-4e7d-b44f-af0a129aefae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:16,438] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:16,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:16,439] [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
Bacteroides faecichinchillae	strain=JCM 17102	GCA_000614145.1	871325	871325	type	True	100.0	1524	1527	95	conclusive
Bacteroides faecichinchillae	strain=DSM 26883	GCA_900129065.1	871325	871325	type	True	99.9736	1521	1527	95	conclusive
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	94.4686	1220	1527	95	below_threshold
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	93.7513	1208	1527	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	81.2683	551	1527	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	81.1781	556	1527	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	81.1765	555	1527	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	80.7347	619	1527	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	80.6754	627	1527	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	79.9902	620	1527	95	below_threshold
Bacteroides luhongzhouii	strain=HF-5141	GCA_009193295.2	2650158	2650158	type	True	79.9585	583	1527	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	79.6601	251	1527	95	below_threshold
Bacteroides nordii	strain=FDAARGOS_1461	GCA_019930665.1	291645	291645	type	True	79.307	346	1527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:16,441] [INFO] DFAST Taxonomy check result was written to GCF_000614145.1_ASM61414v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:16,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:16,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:16,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83fd30d6-2434-4e7d-b44f-af0a129aefae/dqc_reference/checkm_data
[2024-01-24 13:28:16,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:16,492] [INFO] Task started: CheckM
[2024-01-24 13:28:16,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000614145.1_ASM61414v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000614145.1_ASM61414v1_genomic.fna/checkm_input GCF_000614145.1_ASM61414v1_genomic.fna/checkm_result
[2024-01-24 13:29:15,028] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:15,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:15,051] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:15,051] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:15,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000614145.1_ASM61414v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:15,052] [INFO] Task started: Blastn
[2024-01-24 13:29:15,052] [INFO] Running command: blastn -query GCF_000614145.1_ASM61414v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83fd30d6-2434-4e7d-b44f-af0a129aefae/dqc_reference/reference_markers_gtdb.fasta -out GCF_000614145.1_ASM61414v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:16,120] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:16,124] [INFO] Selected 12 target genomes.
[2024-01-24 13:29:16,125] [INFO] Target genome list was writen to GCF_000614145.1_ASM61414v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:16,196] [INFO] Task started: fastANI
[2024-01-24 13:29:16,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgc29c5bbd-9abb-4582-92ec-2e799e82140d/GCF_000614145.1_ASM61414v1_genomic.fna.gz --refList GCF_000614145.1_ASM61414v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000614145.1_ASM61414v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:28,996] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:29,008] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:29,008] [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_000614145.1	s__Bacteroides faecichinchillae	100.0	1524	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.89	99.80	0.96	0.92	3	conclusive
GCF_900155865.1	s__Bacteroides bouchesdurhonensis	94.473	1219	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.60	98.60	0.88	0.88	2	-
GCF_003865075.1	s__Bacteroides faecalis	93.7066	1212	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001688725.2	s__Bacteroides caecimuris	81.201	550	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCF_014750685.1	s__Bacteroides sp014750685	80.7412	593	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314995.1	s__Bacteroides ovatus	80.7163	623	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	80.5622	607	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_900106755.1	s__Bacteroides faecis	80.3724	656	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.27	98.92	0.88	0.84	29	-
GCA_902362375.1	s__Bacteroides sp902362375	80.1206	598	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.74	98.46	0.82	0.77	13	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	79.9968	617	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_009193295.2	s__Bacteroides luhongzhouii	79.9585	583	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.19	98.73	0.86	0.78	4	-
GCA_000613385.1	s__Bacteroides acidifaciens	79.9184	503	1527	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:29,011] [INFO] GTDB search result was written to GCF_000614145.1_ASM61414v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:29,012] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:29,017] [INFO] DFAST_QC result json was written to GCF_000614145.1_ASM61414v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:29,018] [INFO] DFAST_QC completed!
[2024-01-24 13:29:29,018] [INFO] Total running time: 0h1m48s