[2023-06-29 23:32:18,891] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:32:18,894] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:32:18,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg6199415d-2b8a-49ed-8fa9-46db5cc499dd/dqc_reference
[2023-06-29 23:32:20,220] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:32:20,221] [INFO] Task started: Prodigal
[2023-06-29 23:32:20,221] [INFO] Running command: gunzip -c /var/lib/cwl/stg2746d3e6-9cc7-470c-b235-d316ab3cf985/GCA_900758595.1_ERS608534_23_genomic.fna.gz | prodigal -d GCA_900758595.1_ERS608534_23_genomic.fna/cds.fna -a GCA_900758595.1_ERS608534_23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:32:26,060] [INFO] Task succeeded: Prodigal
[2023-06-29 23:32:26,061] [INFO] Task started: HMMsearch
[2023-06-29 23:32:26,061] [INFO] Running command: hmmsearch --tblout GCA_900758595.1_ERS608534_23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6199415d-2b8a-49ed-8fa9-46db5cc499dd/dqc_reference/reference_markers.hmm GCA_900758595.1_ERS608534_23_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:32:26,340] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:32:26,342] [INFO] Found 6/6 markers.
[2023-06-29 23:32:26,364] [INFO] Query marker FASTA was written to GCA_900758595.1_ERS608534_23_genomic.fna/markers.fasta
[2023-06-29 23:32:26,364] [INFO] Task started: Blastn
[2023-06-29 23:32:26,364] [INFO] Running command: blastn -query GCA_900758595.1_ERS608534_23_genomic.fna/markers.fasta -db /var/lib/cwl/stg6199415d-2b8a-49ed-8fa9-46db5cc499dd/dqc_reference/reference_markers.fasta -out GCA_900758595.1_ERS608534_23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:32:27,077] [INFO] Task succeeded: Blastn
[2023-06-29 23:32:27,080] [INFO] Selected 24 target genomes.
[2023-06-29 23:32:27,081] [INFO] Target genome list was writen to GCA_900758595.1_ERS608534_23_genomic.fna/target_genomes.txt
[2023-06-29 23:32:27,082] [INFO] Task started: fastANI
[2023-06-29 23:32:27,082] [INFO] Running command: fastANI --query /var/lib/cwl/stg2746d3e6-9cc7-470c-b235-d316ab3cf985/GCA_900758595.1_ERS608534_23_genomic.fna.gz --refList GCA_900758595.1_ERS608534_23_genomic.fna/target_genomes.txt --output GCA_900758595.1_ERS608534_23_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:32:36,713] [INFO] Task succeeded: fastANI
[2023-06-29 23:32:36,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6199415d-2b8a-49ed-8fa9-46db5cc499dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:32:36,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6199415d-2b8a-49ed-8fa9-46db5cc499dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:32:36,730] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:32:36,730] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:32:36,730] [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
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	77.3225	66	565	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	77.3216	67	565	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.2998	71	565	95	below_threshold
Berryella intestinalis	strain=68-1-3	GCA_000814825.1	1531429	1531429	type	True	77.1915	53	565	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.1801	73	565	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	77.01	72	565	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_016865385.1	394340	446660	type	True	77.0062	89	565	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	76.9836	91	565	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_003428485.1	394340	446660	type	True	76.9821	89	565	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	76.9445	74	565	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	76.929	89	565	95	below_threshold
Raoultibacter timonensis	strain=Marseille-P3277	GCA_900240215.1	1907662	1907662	type	True	76.794	77	565	95	below_threshold
Slackia equolifaciens	strain=DSM 24851	GCA_003725995.1	498718	498718	type	True	76.7837	61	565	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	76.7633	64	565	95	below_threshold
Adlercreutzia equolifaciens subsp. equolifaciens	strain=DSM 19450	GCA_000478885.1	2864143	446660	type	True	76.6768	86	565	95	below_threshold
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	76.5251	54	565	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:32:36,732] [INFO] DFAST Taxonomy check result was written to GCA_900758595.1_ERS608534_23_genomic.fna/tc_result.tsv
[2023-06-29 23:32:36,733] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:32:36,733] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:32:36,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6199415d-2b8a-49ed-8fa9-46db5cc499dd/dqc_reference/checkm_data
[2023-06-29 23:32:36,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:32:36,760] [INFO] Task started: CheckM
[2023-06-29 23:32:36,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900758595.1_ERS608534_23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900758595.1_ERS608534_23_genomic.fna/checkm_input GCA_900758595.1_ERS608534_23_genomic.fna/checkm_result
[2023-06-29 23:32:59,565] [INFO] Task succeeded: CheckM
[2023-06-29 23:32:59,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:32:59,586] [INFO] ===== Completeness check finished =====
[2023-06-29 23:32:59,587] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:32:59,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900758595.1_ERS608534_23_genomic.fna/markers.fasta)
[2023-06-29 23:32:59,588] [INFO] Task started: Blastn
[2023-06-29 23:32:59,588] [INFO] Running command: blastn -query GCA_900758595.1_ERS608534_23_genomic.fna/markers.fasta -db /var/lib/cwl/stg6199415d-2b8a-49ed-8fa9-46db5cc499dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_900758595.1_ERS608534_23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:33:00,674] [INFO] Task succeeded: Blastn
[2023-06-29 23:33:00,678] [INFO] Selected 13 target genomes.
[2023-06-29 23:33:00,678] [INFO] Target genome list was writen to GCA_900758595.1_ERS608534_23_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:33:00,683] [INFO] Task started: fastANI
[2023-06-29 23:33:00,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg2746d3e6-9cc7-470c-b235-d316ab3cf985/GCA_900758595.1_ERS608534_23_genomic.fna.gz --refList GCA_900758595.1_ERS608534_23_genomic.fna/target_genomes_gtdb.txt --output GCA_900758595.1_ERS608534_23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:33:05,474] [INFO] Task succeeded: fastANI
[2023-06-29 23:33:05,483] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:33:05,483] [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_900544245.1	s__QAMH01 sp900544245	97.356	458	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	97.45	97.43	0.84	0.81	3	conclusive
GCA_003149935.1	s__QAMH01 sp003149935	86.2546	469	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	96.22	96.22	0.86	0.86	2	-
GCA_900756605.1	s__QAMH01 sp900756605	86.0116	278	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	97.24	97.24	0.74	0.74	2	-
GCA_900556425.1	s__QAMH01 sp900556425	85.7203	246	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783175.1	s__CACZQA01 sp902783175	78.7574	127	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__CACZQA01	95.0	97.45	97.17	0.71	0.71	3	-
GCA_900758075.1	s__CACZQA01 sp900758075	78.6211	120	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__CACZQA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783925.1	s__QAMH01 sp902783925	77.7738	135	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777325.1	s__UBA1367 sp902777325	77.6217	66	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902778135.1	s__UBA1367 sp902778135	77.2668	56	565	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.30	98.30	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-29 23:33:05,485] [INFO] GTDB search result was written to GCA_900758595.1_ERS608534_23_genomic.fna/result_gtdb.tsv
[2023-06-29 23:33:05,486] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:33:05,490] [INFO] DFAST_QC result json was written to GCA_900758595.1_ERS608534_23_genomic.fna/dqc_result.json
[2023-06-29 23:33:05,490] [INFO] DFAST_QC completed!
[2023-06-29 23:33:05,491] [INFO] Total running time: 0h0m47s