[2023-06-29 15:40:05,902] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:40:05,905] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:40:05,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a920f22-7bc3-4e33-b71c-468a1a48ca34/dqc_reference
[2023-06-29 15:40:07,623] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:40:07,624] [INFO] Task started: Prodigal
[2023-06-29 15:40:07,625] [INFO] Running command: gunzip -c /var/lib/cwl/stge6ae4604-e71e-4355-9481-cfff1c95183a/GCA_023413175.1_ASM2341317v1_genomic.fna.gz | prodigal -d GCA_023413175.1_ASM2341317v1_genomic.fna/cds.fna -a GCA_023413175.1_ASM2341317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:40:13,996] [INFO] Task succeeded: Prodigal
[2023-06-29 15:40:13,997] [INFO] Task started: HMMsearch
[2023-06-29 15:40:13,997] [INFO] Running command: hmmsearch --tblout GCA_023413175.1_ASM2341317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a920f22-7bc3-4e33-b71c-468a1a48ca34/dqc_reference/reference_markers.hmm GCA_023413175.1_ASM2341317v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:40:14,288] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:40:14,289] [INFO] Found 6/6 markers.
[2023-06-29 15:40:14,327] [INFO] Query marker FASTA was written to GCA_023413175.1_ASM2341317v1_genomic.fna/markers.fasta
[2023-06-29 15:40:14,328] [INFO] Task started: Blastn
[2023-06-29 15:40:14,328] [INFO] Running command: blastn -query GCA_023413175.1_ASM2341317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a920f22-7bc3-4e33-b71c-468a1a48ca34/dqc_reference/reference_markers.fasta -out GCA_023413175.1_ASM2341317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:40:15,014] [INFO] Task succeeded: Blastn
[2023-06-29 15:40:15,019] [INFO] Selected 21 target genomes.
[2023-06-29 15:40:15,019] [INFO] Target genome list was writen to GCA_023413175.1_ASM2341317v1_genomic.fna/target_genomes.txt
[2023-06-29 15:40:15,020] [INFO] Task started: fastANI
[2023-06-29 15:40:15,020] [INFO] Running command: fastANI --query /var/lib/cwl/stge6ae4604-e71e-4355-9481-cfff1c95183a/GCA_023413175.1_ASM2341317v1_genomic.fna.gz --refList GCA_023413175.1_ASM2341317v1_genomic.fna/target_genomes.txt --output GCA_023413175.1_ASM2341317v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:40:26,642] [INFO] Task succeeded: fastANI
[2023-06-29 15:40:26,643] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a920f22-7bc3-4e33-b71c-468a1a48ca34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:40:26,643] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a920f22-7bc3-4e33-b71c-468a1a48ca34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:40:26,658] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 15:40:26,658] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 15:40:26,658] [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
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	98.5135	691	776	95	conclusive
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	79.1892	185	776	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	79.1721	186	776	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	79.1053	184	776	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.3857	192	776	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.6499	142	776	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.5237	104	776	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	77.2803	111	776	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.6929	76	776	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	76.3707	64	776	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	76.3701	66	776	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.231	68	776	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	76.0094	72	776	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.0043	60	776	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	76.0025	60	776	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	75.9773	61	776	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	75.9659	60	776	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:40:26,662] [INFO] DFAST Taxonomy check result was written to GCA_023413175.1_ASM2341317v1_genomic.fna/tc_result.tsv
[2023-06-29 15:40:26,663] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:40:26,663] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:40:26,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a920f22-7bc3-4e33-b71c-468a1a48ca34/dqc_reference/checkm_data
[2023-06-29 15:40:26,665] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:40:26,709] [INFO] Task started: CheckM
[2023-06-29 15:40:26,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023413175.1_ASM2341317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023413175.1_ASM2341317v1_genomic.fna/checkm_input GCA_023413175.1_ASM2341317v1_genomic.fna/checkm_result
[2023-06-29 15:40:52,591] [INFO] Task succeeded: CheckM
[2023-06-29 15:40:52,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:40:52,613] [INFO] ===== Completeness check finished =====
[2023-06-29 15:40:52,614] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:40:52,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023413175.1_ASM2341317v1_genomic.fna/markers.fasta)
[2023-06-29 15:40:52,614] [INFO] Task started: Blastn
[2023-06-29 15:40:52,615] [INFO] Running command: blastn -query GCA_023413175.1_ASM2341317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a920f22-7bc3-4e33-b71c-468a1a48ca34/dqc_reference/reference_markers_gtdb.fasta -out GCA_023413175.1_ASM2341317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:40:53,688] [INFO] Task succeeded: Blastn
[2023-06-29 15:40:53,711] [INFO] Selected 10 target genomes.
[2023-06-29 15:40:53,712] [INFO] Target genome list was writen to GCA_023413175.1_ASM2341317v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:40:53,717] [INFO] Task started: fastANI
[2023-06-29 15:40:53,718] [INFO] Running command: fastANI --query /var/lib/cwl/stge6ae4604-e71e-4355-9481-cfff1c95183a/GCA_023413175.1_ASM2341317v1_genomic.fna.gz --refList GCA_023413175.1_ASM2341317v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023413175.1_ASM2341317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:40:59,019] [INFO] Task succeeded: fastANI
[2023-06-29 15:40:59,031] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:40:59,032] [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_001406815.1	s__Agathobacter faecis	98.5135	691	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	conclusive
GCA_002474415.1	s__Agathobacter sp002474415	91.2406	458	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363675.1	s__Agathobacter sp000434275	81.2351	338	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.18	99.14	0.93	0.89	5	-
GCA_900550545.1	s__Agathobacter sp900550545	80.5045	298	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552085.1	s__Agathobacter sp900552085	79.8211	243	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_900549895.1	s__Agathobacter sp900549895	79.0155	206	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543445.1	s__Agathobacter sp900543445	78.7997	249	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
GCF_009695765.1	s__VUNI01 sp009695765	78.3857	192	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225345.1	s__Roseburia hominis	77.6499	142	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCA_910587655.1	s__Agathobacter sp910587655	77.4127	176	776	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:40:59,048] [INFO] GTDB search result was written to GCA_023413175.1_ASM2341317v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:40:59,049] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:40:59,056] [INFO] DFAST_QC result json was written to GCA_023413175.1_ASM2341317v1_genomic.fna/dqc_result.json
[2023-06-29 15:40:59,056] [INFO] DFAST_QC completed!
[2023-06-29 15:40:59,056] [INFO] Total running time: 0h0m53s