[2023-06-14 02:10:52,557] [INFO] DFAST_QC pipeline started.
[2023-06-14 02:10:52,559] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 02:10:52,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a3b4282-35e2-48fc-a438-27f62d4e85b2/dqc_reference
[2023-06-14 02:10:53,924] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 02:10:53,925] [INFO] Task started: Prodigal
[2023-06-14 02:10:53,925] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5e9e2eb-295a-4c9a-bacb-c47aa97aa1db/GCA_022775005.1_ASM2277500v1_genomic.fna.gz | prodigal -d GCA_022775005.1_ASM2277500v1_genomic.fna/cds.fna -a GCA_022775005.1_ASM2277500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 02:11:12,569] [INFO] Task succeeded: Prodigal
[2023-06-14 02:11:12,570] [INFO] Task started: HMMsearch
[2023-06-14 02:11:12,570] [INFO] Running command: hmmsearch --tblout GCA_022775005.1_ASM2277500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a3b4282-35e2-48fc-a438-27f62d4e85b2/dqc_reference/reference_markers.hmm GCA_022775005.1_ASM2277500v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 02:11:12,843] [INFO] Task succeeded: HMMsearch
[2023-06-14 02:11:12,845] [INFO] Found 6/6 markers.
[2023-06-14 02:11:12,882] [INFO] Query marker FASTA was written to GCA_022775005.1_ASM2277500v1_genomic.fna/markers.fasta
[2023-06-14 02:11:12,883] [INFO] Task started: Blastn
[2023-06-14 02:11:12,883] [INFO] Running command: blastn -query GCA_022775005.1_ASM2277500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a3b4282-35e2-48fc-a438-27f62d4e85b2/dqc_reference/reference_markers.fasta -out GCA_022775005.1_ASM2277500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 02:11:13,502] [INFO] Task succeeded: Blastn
[2023-06-14 02:11:13,506] [INFO] Selected 21 target genomes.
[2023-06-14 02:11:13,507] [INFO] Target genome list was writen to GCA_022775005.1_ASM2277500v1_genomic.fna/target_genomes.txt
[2023-06-14 02:11:13,514] [INFO] Task started: fastANI
[2023-06-14 02:11:13,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5e9e2eb-295a-4c9a-bacb-c47aa97aa1db/GCA_022775005.1_ASM2277500v1_genomic.fna.gz --refList GCA_022775005.1_ASM2277500v1_genomic.fna/target_genomes.txt --output GCA_022775005.1_ASM2277500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 02:11:28,181] [INFO] Task succeeded: fastANI
[2023-06-14 02:11:28,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a3b4282-35e2-48fc-a438-27f62d4e85b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 02:11:28,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a3b4282-35e2-48fc-a438-27f62d4e85b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 02:11:28,192] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 02:11:28,192] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 02:11:28,192] [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
Parabacteroides merdae	strain=ATCC 43184	GCA_025151215.1	46503	46503	type	True	78.1192	130	993	95	below_threshold
Parabacteroides merdae	strain=ATCC 43184	GCA_000154105.1	46503	46503	type	True	78.0831	132	993	95	below_threshold
Parabacteroides distasonis	strain=ATCC 8503	GCA_000012845.1	823	823	type	True	78.0447	223	993	95	below_threshold
Parabacteroides distasonis	strain=NCTC11152	GCA_900445525.1	823	823	type	True	78.0182	220	993	95	below_threshold
Parabacteroides distasonis	strain=FDAARGOS_1565	GCA_020735945.1	823	823	type	True	77.9953	226	993	95	below_threshold
Parabacteroides acidifaciens	strain=426-9	GCA_003363715.1	2290935	2290935	type	True	77.5194	135	993	95	below_threshold
Parabacteroides acidifaciens	strain=426_9	GCA_014385205.1	2290935	2290935	type	True	77.5087	134	993	95	below_threshold
Parabacteroides gordonii	strain=MS-1	GCA_000969825.1	574930	574930	type	True	77.4061	125	993	95	below_threshold
Parabacteroides gordonii	strain=FDAARGOS_1522	GCA_020297465.1	574930	574930	type	True	77.3294	122	993	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 02:11:28,195] [INFO] DFAST Taxonomy check result was written to GCA_022775005.1_ASM2277500v1_genomic.fna/tc_result.tsv
[2023-06-14 02:11:28,196] [INFO] ===== Taxonomy check completed =====
[2023-06-14 02:11:28,196] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 02:11:28,197] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a3b4282-35e2-48fc-a438-27f62d4e85b2/dqc_reference/checkm_data
[2023-06-14 02:11:28,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 02:11:28,233] [INFO] Task started: CheckM
[2023-06-14 02:11:28,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022775005.1_ASM2277500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022775005.1_ASM2277500v1_genomic.fna/checkm_input GCA_022775005.1_ASM2277500v1_genomic.fna/checkm_result
[2023-06-14 02:12:21,848] [INFO] Task succeeded: CheckM
[2023-06-14 02:12:21,849] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 02:12:21,870] [INFO] ===== Completeness check finished =====
[2023-06-14 02:12:21,871] [INFO] ===== Start GTDB Search =====
[2023-06-14 02:12:21,871] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022775005.1_ASM2277500v1_genomic.fna/markers.fasta)
[2023-06-14 02:12:21,871] [INFO] Task started: Blastn
[2023-06-14 02:12:21,872] [INFO] Running command: blastn -query GCA_022775005.1_ASM2277500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8a3b4282-35e2-48fc-a438-27f62d4e85b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_022775005.1_ASM2277500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 02:12:22,703] [INFO] Task succeeded: Blastn
[2023-06-14 02:12:22,708] [INFO] Selected 20 target genomes.
[2023-06-14 02:12:22,708] [INFO] Target genome list was writen to GCA_022775005.1_ASM2277500v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 02:12:22,744] [INFO] Task started: fastANI
[2023-06-14 02:12:22,744] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5e9e2eb-295a-4c9a-bacb-c47aa97aa1db/GCA_022775005.1_ASM2277500v1_genomic.fna.gz --refList GCA_022775005.1_ASM2277500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022775005.1_ASM2277500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 02:12:34,733] [INFO] Task succeeded: fastANI
[2023-06-14 02:12:34,751] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 02:12:34,752] [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
GCA_900770835.1	s__Parabacteroides sp900770835	87.1655	653	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012845.1	s__Parabacteroides distasonis	78.0365	223	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.16	96.57	0.86	0.75	191	-
GCF_004793765.1	s__Parabacteroides distasonis_A	77.9555	220	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.06	98.88	0.88	0.86	4	-
GCF_011038785.1	s__Parabacteroides sp011038785	77.95	186	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287585.1	s__Parabacteroides sp014287585	77.6732	139	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	99.33	98.97	0.95	0.91	4	-
GCA_019114945.1	s__Parabacteroides intestinigallinarum	77.6531	205	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003363715.1	s__Parabacteroides acidifaciens	77.5138	136	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	98.21	97.25	0.91	0.84	7	-
GCA_000436495.1	s__Parabacteroides faecavium	77.4688	93	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	96.87	96.42	0.81	0.77	5	-
GCA_900552415.1	s__Parabacteroides intestinipullorum	77.3014	139	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	97.21	97.01	0.88	0.87	3	-
GCA_004562445.1	s__Parabacteroides sp004562445	77.2923	147	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937385.1	s__Parabacteroides sp017937385	77.1011	133	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Tannerellaceae;g__Parabacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130135.1	s__Bacteroides togonis	76.8661	57	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.34	96.94	0.82	0.80	8	-
GCF_900128475.1	s__Bacteroides massiliensis	76.5412	52	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCA_004558305.1	s__Phocaeicola plebeius_B	76.3053	50	993	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 02:12:34,754] [INFO] GTDB search result was written to GCA_022775005.1_ASM2277500v1_genomic.fna/result_gtdb.tsv
[2023-06-14 02:12:34,755] [INFO] ===== GTDB Search completed =====
[2023-06-14 02:12:34,760] [INFO] DFAST_QC result json was written to GCA_022775005.1_ASM2277500v1_genomic.fna/dqc_result.json
[2023-06-14 02:12:34,760] [INFO] DFAST_QC completed!
[2023-06-14 02:12:34,760] [INFO] Total running time: 0h1m42s