[2023-06-17 11:26:01,984] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:01,987] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:01,987] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9af0962-e900-4f78-8d4a-edfafa4132ab/dqc_reference
[2023-06-17 11:26:03,264] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:03,264] [INFO] Task started: Prodigal
[2023-06-17 11:26:03,265] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbc010b7-963a-466b-a778-d954117d55a0/GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna.gz | prodigal -d GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/cds.fna -a GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:26:23,404] [INFO] Task succeeded: Prodigal
[2023-06-17 11:26:23,405] [INFO] Task started: HMMsearch
[2023-06-17 11:26:23,405] [INFO] Running command: hmmsearch --tblout GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9af0962-e900-4f78-8d4a-edfafa4132ab/dqc_reference/reference_markers.hmm GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:26:23,783] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:26:23,785] [INFO] Found 6/6 markers.
[2023-06-17 11:26:23,840] [INFO] Query marker FASTA was written to GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/markers.fasta
[2023-06-17 11:26:23,840] [INFO] Task started: Blastn
[2023-06-17 11:26:23,840] [INFO] Running command: blastn -query GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9af0962-e900-4f78-8d4a-edfafa4132ab/dqc_reference/reference_markers.fasta -out GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:26:24,511] [INFO] Task succeeded: Blastn
[2023-06-17 11:26:24,516] [INFO] Selected 22 target genomes.
[2023-06-17 11:26:24,516] [INFO] Target genome list was writen to GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/target_genomes.txt
[2023-06-17 11:26:24,522] [INFO] Task started: fastANI
[2023-06-17 11:26:24,522] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc010b7-963a-466b-a778-d954117d55a0/GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna.gz --refList GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/target_genomes.txt --output GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:26:37,902] [INFO] Task succeeded: fastANI
[2023-06-17 11:26:37,903] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9af0962-e900-4f78-8d4a-edfafa4132ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:26:37,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9af0962-e900-4f78-8d4a-edfafa4132ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:26:37,923] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:26:37,923] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:26:37,923] [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
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	86.8523	710	1228	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	86.7088	700	1228	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	86.6611	685	1228	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	84.301	572	1228	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	79.0625	154	1228	95	below_threshold
Prevotella ihumii	strain=Marseille-P3385	GCA_900155655.1	1917878	1917878	type	True	78.0216	69	1228	95	below_threshold
Prevotella scopos	strain=W2052	GCA_001683355.1	589437	589437	type	True	77.7846	99	1228	95	below_threshold
Prevotella scopos	strain=DSM 22613	GCA_900129535.1	589437	589437	type	True	77.7675	99	1228	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.7651	114	1228	95	below_threshold
Prevotella scopos	strain=W2052	GCA_018127785.1	589437	589437	type	True	77.765	99	1228	95	below_threshold
Prevotella scopos	strain=JCM 17725	GCA_000614285.1	589437	589437	type	True	77.755	97	1228	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	77.5556	135	1228	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	77.5413	77	1228	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.5324	143	1228	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.4876	142	1228	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	77.1185	110	1228	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	77.08	109	1228	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	77.0063	97	1228	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	76.8348	98	1228	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:26:37,926] [INFO] DFAST Taxonomy check result was written to GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/tc_result.tsv
[2023-06-17 11:26:37,927] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:26:37,927] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:26:37,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9af0962-e900-4f78-8d4a-edfafa4132ab/dqc_reference/checkm_data
[2023-06-17 11:26:37,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:26:37,973] [INFO] Task started: CheckM
[2023-06-17 11:26:37,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/checkm_input GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/checkm_result
[2023-06-17 11:27:35,604] [INFO] Task succeeded: CheckM
[2023-06-17 11:27:35,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 11:27:35,626] [INFO] ===== Completeness check finished =====
[2023-06-17 11:27:35,626] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:27:35,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/markers.fasta)
[2023-06-17 11:27:35,627] [INFO] Task started: Blastn
[2023-06-17 11:27:35,627] [INFO] Running command: blastn -query GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9af0962-e900-4f78-8d4a-edfafa4132ab/dqc_reference/reference_markers_gtdb.fasta -out GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:36,499] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:36,504] [INFO] Selected 12 target genomes.
[2023-06-17 11:27:36,504] [INFO] Target genome list was writen to GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:27:36,512] [INFO] Task started: fastANI
[2023-06-17 11:27:36,513] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc010b7-963a-466b-a778-d954117d55a0/GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna.gz --refList GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/target_genomes_gtdb.txt --output GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:27:46,245] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:46,260] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:27:46,260] [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_009494395.1	s__Prevotella sp900546535	96.834	966	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	conclusive
GCA_900556795.1	s__Prevotella sp900556795	93.7213	399	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.16	0.81	0.77	3	-
GCA_900770515.1	s__Prevotella sp900770515	90.4002	381	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224675.1	s__Prevotella copri_A	88.6591	767	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_900544825.1	s__Prevotella sp900544825	87.879	702	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_900551985.1	s__Prevotella sp900551985	87.8228	630	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCA_019249655.1	s__Prevotella sp900767615	87.8156	780	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_015074785.1	s__Prevotella sp015074785	87.3162	741	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_019127135.1	s__Prevotella sp900551275	87.1709	749	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCF_000157935.1	s__Prevotella copri	86.8657	709	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900557035.1	s__Prevotella sp900557035	86.5318	489	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_900765465.1	s__Prevotella sp900765465	84.4647	338	1228	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:27:46,262] [INFO] GTDB search result was written to GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/result_gtdb.tsv
[2023-06-17 11:27:46,263] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:27:46,267] [INFO] DFAST_QC result json was written to GCA_905206415.1_ERR1600572-mag-bin.31_genomic.fna/dqc_result.json
[2023-06-17 11:27:46,267] [INFO] DFAST_QC completed!
[2023-06-17 11:27:46,267] [INFO] Total running time: 0h1m44s