[2023-06-16 20:04:30,982] [INFO] DFAST_QC pipeline started.
[2023-06-16 20:04:30,985] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 20:04:30,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgf81da008-3af1-4939-9b5f-cd05d7f687e9/dqc_reference
[2023-06-16 20:04:32,429] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 20:04:32,430] [INFO] Task started: Prodigal
[2023-06-16 20:04:32,430] [INFO] Running command: gunzip -c /var/lib/cwl/stg96139f47-41bc-459a-9e33-b56ed8593dfd/GCA_003522185.1_ASM352218v1_genomic.fna.gz | prodigal -d GCA_003522185.1_ASM352218v1_genomic.fna/cds.fna -a GCA_003522185.1_ASM352218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 20:04:39,203] [INFO] Task succeeded: Prodigal
[2023-06-16 20:04:39,204] [INFO] Task started: HMMsearch
[2023-06-16 20:04:39,204] [INFO] Running command: hmmsearch --tblout GCA_003522185.1_ASM352218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf81da008-3af1-4939-9b5f-cd05d7f687e9/dqc_reference/reference_markers.hmm GCA_003522185.1_ASM352218v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 20:04:39,392] [INFO] Task succeeded: HMMsearch
[2023-06-16 20:04:39,393] [INFO] Found 6/6 markers.
[2023-06-16 20:04:39,416] [INFO] Query marker FASTA was written to GCA_003522185.1_ASM352218v1_genomic.fna/markers.fasta
[2023-06-16 20:04:39,417] [INFO] Task started: Blastn
[2023-06-16 20:04:39,417] [INFO] Running command: blastn -query GCA_003522185.1_ASM352218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf81da008-3af1-4939-9b5f-cd05d7f687e9/dqc_reference/reference_markers.fasta -out GCA_003522185.1_ASM352218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:04:40,069] [INFO] Task succeeded: Blastn
[2023-06-16 20:04:40,083] [INFO] Selected 14 target genomes.
[2023-06-16 20:04:40,084] [INFO] Target genome list was writen to GCA_003522185.1_ASM352218v1_genomic.fna/target_genomes.txt
[2023-06-16 20:04:40,086] [INFO] Task started: fastANI
[2023-06-16 20:04:40,086] [INFO] Running command: fastANI --query /var/lib/cwl/stg96139f47-41bc-459a-9e33-b56ed8593dfd/GCA_003522185.1_ASM352218v1_genomic.fna.gz --refList GCA_003522185.1_ASM352218v1_genomic.fna/target_genomes.txt --output GCA_003522185.1_ASM352218v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 20:04:47,289] [INFO] Task succeeded: fastANI
[2023-06-16 20:04:47,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf81da008-3af1-4939-9b5f-cd05d7f687e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 20:04:47,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf81da008-3af1-4939-9b5f-cd05d7f687e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 20:04:47,298] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 20:04:47,298] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 20:04:47,298] [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
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	79.0129	199	733	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	78.6803	178	733	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	78.5412	183	733	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	78.429	256	733	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.3435	252	733	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	77.9333	118	733	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	77.7554	173	733	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.1009	123	733	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 20:04:47,300] [INFO] DFAST Taxonomy check result was written to GCA_003522185.1_ASM352218v1_genomic.fna/tc_result.tsv
[2023-06-16 20:04:47,301] [INFO] ===== Taxonomy check completed =====
[2023-06-16 20:04:47,301] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 20:04:47,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf81da008-3af1-4939-9b5f-cd05d7f687e9/dqc_reference/checkm_data
[2023-06-16 20:04:47,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 20:04:47,330] [INFO] Task started: CheckM
[2023-06-16 20:04:47,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003522185.1_ASM352218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003522185.1_ASM352218v1_genomic.fna/checkm_input GCA_003522185.1_ASM352218v1_genomic.fna/checkm_result
[2023-06-16 20:05:11,557] [INFO] Task succeeded: CheckM
[2023-06-16 20:05:11,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.68%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 20:05:11,579] [INFO] ===== Completeness check finished =====
[2023-06-16 20:05:11,579] [INFO] ===== Start GTDB Search =====
[2023-06-16 20:05:11,580] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003522185.1_ASM352218v1_genomic.fna/markers.fasta)
[2023-06-16 20:05:11,580] [INFO] Task started: Blastn
[2023-06-16 20:05:11,580] [INFO] Running command: blastn -query GCA_003522185.1_ASM352218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf81da008-3af1-4939-9b5f-cd05d7f687e9/dqc_reference/reference_markers_gtdb.fasta -out GCA_003522185.1_ASM352218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 20:05:12,789] [INFO] Task succeeded: Blastn
[2023-06-16 20:05:12,793] [INFO] Selected 17 target genomes.
[2023-06-16 20:05:12,793] [INFO] Target genome list was writen to GCA_003522185.1_ASM352218v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 20:05:12,829] [INFO] Task started: fastANI
[2023-06-16 20:05:12,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg96139f47-41bc-459a-9e33-b56ed8593dfd/GCA_003522185.1_ASM352218v1_genomic.fna.gz --refList GCA_003522185.1_ASM352218v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003522185.1_ASM352218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 20:05:22,051] [INFO] Task succeeded: fastANI
[2023-06-16 20:05:22,064] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 20:05:22,064] [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_003324125.1	s__Gemmiger qucibialis	98.2571	609	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.44	97.30	0.87	0.66	39	conclusive
GCF_018784445.1	s__Gemmiger sp900540775	81.1106	366	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.04	97.97	0.87	0.81	8	-
GCA_900539695.1	s__Gemmiger sp900539695	80.1056	313	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.42	97.91	0.86	0.79	8	-
GCA_004554775.1	s__Gemmiger variabilis_B	80.0271	358	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.40	97.89	0.89	0.88	3	-
GCA_900772715.1	s__Gemmiger sp900772715	79.891	179	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004561545.1	s__Gemmiger sp004561545	79.7575	274	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214345.1	s__Gemmiger sp905214345	79.111	301	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900095.1	s__Gemmiger formicilis_A	78.9798	310	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545545.1	s__Gemmiger sp900545545	78.9459	279	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	96.26	96.20	0.77	0.76	3	-
GCA_019116445.1	s__Gemmiger excrementigallinarum	78.8729	232	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003343905.1	s__Gemmiger variabilis_C	78.7431	281	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114415.1	s__Gemmiger faecavium	78.7368	270	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904374465.1	s__Gemmiger sp904374465	78.7327	253	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014982805.1	s__Gemmiger sp014982805	78.5618	275	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116485.1	s__Gemmiger excrementavium	78.4294	278	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115045.1	s__Gemmiger excrementipullorum	78.4087	263	733	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 20:05:22,066] [INFO] GTDB search result was written to GCA_003522185.1_ASM352218v1_genomic.fna/result_gtdb.tsv
[2023-06-16 20:05:22,067] [INFO] ===== GTDB Search completed =====
[2023-06-16 20:05:22,073] [INFO] DFAST_QC result json was written to GCA_003522185.1_ASM352218v1_genomic.fna/dqc_result.json
[2023-06-16 20:05:22,074] [INFO] DFAST_QC completed!
[2023-06-16 20:05:22,074] [INFO] Total running time: 0h0m51s