[2023-06-05 04:03:15,130] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:03:15,133] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:03:15,133] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d285998-d172-4274-b36e-9a363601544b/dqc_reference
[2023-06-05 04:03:17,027] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:03:17,028] [INFO] Task started: Prodigal
[2023-06-05 04:03:17,029] [INFO] Running command: gunzip -c /var/lib/cwl/stge557b3b7-6a63-49b1-9b52-88b433001187/GCA_004557705.1_ASM455770v1_genomic.fna.gz | prodigal -d GCA_004557705.1_ASM455770v1_genomic.fna/cds.fna -a GCA_004557705.1_ASM455770v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:03:32,987] [INFO] Task succeeded: Prodigal
[2023-06-05 04:03:32,988] [INFO] Task started: HMMsearch
[2023-06-05 04:03:32,988] [INFO] Running command: hmmsearch --tblout GCA_004557705.1_ASM455770v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d285998-d172-4274-b36e-9a363601544b/dqc_reference/reference_markers.hmm GCA_004557705.1_ASM455770v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:03:33,258] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:03:33,259] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge557b3b7-6a63-49b1-9b52-88b433001187/GCA_004557705.1_ASM455770v1_genomic.fna.gz]
[2023-06-05 04:03:33,285] [INFO] Query marker FASTA was written to GCA_004557705.1_ASM455770v1_genomic.fna/markers.fasta
[2023-06-05 04:03:33,285] [INFO] Task started: Blastn
[2023-06-05 04:03:33,285] [INFO] Running command: blastn -query GCA_004557705.1_ASM455770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d285998-d172-4274-b36e-9a363601544b/dqc_reference/reference_markers.fasta -out GCA_004557705.1_ASM455770v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:03:33,925] [INFO] Task succeeded: Blastn
[2023-06-05 04:03:33,929] [INFO] Selected 18 target genomes.
[2023-06-05 04:03:33,929] [INFO] Target genome list was writen to GCA_004557705.1_ASM455770v1_genomic.fna/target_genomes.txt
[2023-06-05 04:03:33,932] [INFO] Task started: fastANI
[2023-06-05 04:03:33,932] [INFO] Running command: fastANI --query /var/lib/cwl/stge557b3b7-6a63-49b1-9b52-88b433001187/GCA_004557705.1_ASM455770v1_genomic.fna.gz --refList GCA_004557705.1_ASM455770v1_genomic.fna/target_genomes.txt --output GCA_004557705.1_ASM455770v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:03:43,182] [INFO] Task succeeded: fastANI
[2023-06-05 04:03:43,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d285998-d172-4274-b36e-9a363601544b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:03:43,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d285998-d172-4274-b36e-9a363601544b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:03:43,195] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 04:03:43,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 04:03:43,196] [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 pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	98.4338	679	830	95	conclusive
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	80.3787	168	830	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	78.7648	94	830	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	78.3142	107	830	95	below_threshold
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	77.756	70	830	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.6798	108	830	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	77.1624	89	830	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	77.1141	69	830	95	below_threshold
Palleniella intestinalis	strain=PINT	GCA_013166595.1	2736291	2736291	type	True	77.0834	70	830	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	76.798	58	830	95	below_threshold
Prevotella fusca	strain=W1435	GCA_018128145.1	589436	589436	type	True	76.7838	58	830	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.5569	68	830	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 04:03:43,198] [INFO] DFAST Taxonomy check result was written to GCA_004557705.1_ASM455770v1_genomic.fna/tc_result.tsv
[2023-06-05 04:03:43,199] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:03:43,199] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:03:43,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d285998-d172-4274-b36e-9a363601544b/dqc_reference/checkm_data
[2023-06-05 04:03:43,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:03:43,239] [INFO] Task started: CheckM
[2023-06-05 04:03:43,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004557705.1_ASM455770v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004557705.1_ASM455770v1_genomic.fna/checkm_input GCA_004557705.1_ASM455770v1_genomic.fna/checkm_result
[2023-06-05 04:04:31,068] [INFO] Task succeeded: CheckM
[2023-06-05 04:04:31,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 04:04:31,094] [INFO] ===== Completeness check finished =====
[2023-06-05 04:04:31,094] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:04:31,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004557705.1_ASM455770v1_genomic.fna/markers.fasta)
[2023-06-05 04:04:31,095] [INFO] Task started: Blastn
[2023-06-05 04:04:31,095] [INFO] Running command: blastn -query GCA_004557705.1_ASM455770v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d285998-d172-4274-b36e-9a363601544b/dqc_reference/reference_markers_gtdb.fasta -out GCA_004557705.1_ASM455770v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:04:32,175] [INFO] Task succeeded: Blastn
[2023-06-05 04:04:32,180] [INFO] Selected 16 target genomes.
[2023-06-05 04:04:32,180] [INFO] Target genome list was writen to GCA_004557705.1_ASM455770v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:04:32,220] [INFO] Task started: fastANI
[2023-06-05 04:04:32,220] [INFO] Running command: fastANI --query /var/lib/cwl/stge557b3b7-6a63-49b1-9b52-88b433001187/GCA_004557705.1_ASM455770v1_genomic.fna.gz --refList GCA_004557705.1_ASM455770v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004557705.1_ASM455770v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:04:40,751] [INFO] Task succeeded: fastANI
[2023-06-05 04:04:40,768] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 04:04:40,768] [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_000834015.1	s__Prevotella pectinovora	98.4656	678	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	conclusive
GCA_900557405.1	s__Prevotella sp900557405	80.8146	309	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.88	97.88	0.76	0.76	2	-
GCF_019052365.1	s__Prevotella sp000434975	80.4741	203	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.22	96.59	0.82	0.74	11	-
GCF_000235885.1	s__Prevotella stercorea	80.3113	170	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.02	96.84	0.81	0.69	8	-
GCA_900772835.1	s__Prevotella sp900772835	80.2189	287	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002314055.1	s__Prevotella sp002314055	79.3875	277	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.08	98.98	0.90	0.84	9	-
GCA_002298545.1	s__Prevotella sp002298545	79.3306	268	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548745.1	s__Prevotella sp900548745	79.2617	283	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.94	97.91	0.83	0.71	3	-
GCA_900544495.1	s__Prevotella sp900544495	78.3871	132	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.45	98.42	0.86	0.82	3	-
GCA_004557285.1	s__Prevotella sp004557285	77.3906	115	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	98.35	0.77	0.77	2	-
GCA_900770395.1	s__Prevotella sp900770395	77.2859	125	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.78	95.78	0.79	0.79	2	-
GCA_000433175.1	s__Prevotella sp000433175	77.2513	109	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	-
GCA_900550365.1	s__Prevotella sp900550365	77.2044	98	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545525.1	s__Prevotella sp900545525	76.9711	133	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCF_016899855.1	s__Prevotella sp000436595	76.8942	111	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	97.50	0.84	0.81	5	-
GCA_902797505.1	s__Prevotella sp902797505	76.1315	53	830	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.08	95.72	0.78	0.72	7	-
--------------------------------------------------------------------------------
[2023-06-05 04:04:40,770] [INFO] GTDB search result was written to GCA_004557705.1_ASM455770v1_genomic.fna/result_gtdb.tsv
[2023-06-05 04:04:40,771] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:04:40,775] [INFO] DFAST_QC result json was written to GCA_004557705.1_ASM455770v1_genomic.fna/dqc_result.json
[2023-06-05 04:04:40,775] [INFO] DFAST_QC completed!
[2023-06-05 04:04:40,775] [INFO] Total running time: 0h1m26s