[2023-06-30 08:36:56,003] [INFO] DFAST_QC pipeline started.
[2023-06-30 08:36:56,007] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 08:36:56,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg50387a4d-6b6c-4bc8-8ccb-ac0380227390/dqc_reference
[2023-06-30 08:36:58,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 08:36:58,203] [INFO] Task started: Prodigal
[2023-06-30 08:36:58,204] [INFO] Running command: gunzip -c /var/lib/cwl/stg771d09aa-8d8c-469c-8ade-0a08a84615a6/GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna.gz | prodigal -d GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/cds.fna -a GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 08:37:00,840] [INFO] Task succeeded: Prodigal
[2023-06-30 08:37:00,840] [INFO] Task started: HMMsearch
[2023-06-30 08:37:00,840] [INFO] Running command: hmmsearch --tblout GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50387a4d-6b6c-4bc8-8ccb-ac0380227390/dqc_reference/reference_markers.hmm GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 08:37:01,056] [INFO] Task succeeded: HMMsearch
[2023-06-30 08:37:01,058] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg771d09aa-8d8c-469c-8ade-0a08a84615a6/GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna.gz]
[2023-06-30 08:37:01,078] [INFO] Query marker FASTA was written to GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta
[2023-06-30 08:37:01,078] [INFO] Task started: Blastn
[2023-06-30 08:37:01,078] [INFO] Running command: blastn -query GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg50387a4d-6b6c-4bc8-8ccb-ac0380227390/dqc_reference/reference_markers.fasta -out GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:37:02,593] [INFO] Task succeeded: Blastn
[2023-06-30 08:37:02,598] [INFO] Selected 12 target genomes.
[2023-06-30 08:37:02,599] [INFO] Target genome list was writen to GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt
[2023-06-30 08:37:02,643] [INFO] Task started: fastANI
[2023-06-30 08:37:02,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg771d09aa-8d8c-469c-8ade-0a08a84615a6/GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt --output GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 08:37:06,128] [INFO] Task succeeded: fastANI
[2023-06-30 08:37:06,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50387a4d-6b6c-4bc8-8ccb-ac0380227390/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 08:37:06,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50387a4d-6b6c-4bc8-8ccb-ac0380227390/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 08:37:06,141] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 08:37:06,142] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 08:37:06,142] [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
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	90.4137	331	431	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	88.3346	319	431	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.6915	139	431	95	below_threshold
Lactobacillus bombicola	strain=R-53102	GCA_900112665.1	1505723	1505723	type	True	78.0791	128	431	95	below_threshold
Lactobacillus bombicola	strain=H70-3	GCA_002916915.1	1505723	1505723	type	True	78.0775	130	431	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	77.7317	69	431	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	77.2796	79	431	95	below_threshold
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	77.1876	80	431	95	below_threshold
Lactobacillus acetotolerans	strain=JCM 3825	GCA_014648715.1	1600	1600	type	True	77.1024	87	431	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 08:37:06,144] [INFO] DFAST Taxonomy check result was written to GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/tc_result.tsv
[2023-06-30 08:37:06,145] [INFO] ===== Taxonomy check completed =====
[2023-06-30 08:37:06,145] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 08:37:06,145] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50387a4d-6b6c-4bc8-8ccb-ac0380227390/dqc_reference/checkm_data
[2023-06-30 08:37:06,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 08:37:06,186] [INFO] Task started: CheckM
[2023-06-30 08:37:06,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/checkm_input GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/checkm_result
[2023-06-30 08:37:23,946] [INFO] Task succeeded: CheckM
[2023-06-30 08:37:23,948] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 08:37:23,969] [INFO] ===== Completeness check finished =====
[2023-06-30 08:37:23,969] [INFO] ===== Start GTDB Search =====
[2023-06-30 08:37:23,970] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta)
[2023-06-30 08:37:23,970] [INFO] Task started: Blastn
[2023-06-30 08:37:23,970] [INFO] Running command: blastn -query GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg50387a4d-6b6c-4bc8-8ccb-ac0380227390/dqc_reference/reference_markers_gtdb.fasta -out GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:37:24,411] [INFO] Task succeeded: Blastn
[2023-06-30 08:37:24,416] [INFO] Selected 11 target genomes.
[2023-06-30 08:37:24,416] [INFO] Target genome list was writen to GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 08:37:24,425] [INFO] Task started: fastANI
[2023-06-30 08:37:24,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg771d09aa-8d8c-469c-8ade-0a08a84615a6/GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 08:37:28,324] [INFO] Task succeeded: fastANI
[2023-06-30 08:37:28,342] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 08:37:28,343] [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_000970755.1	s__Lactobacillus kimbladii_A	92.4629	344	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	90.7514	346	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
GCF_014323605.1	s__Lactobacillus kimbladii_B	90.4405	324	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967195.1	s__Lactobacillus kullabergensis	89.7612	341	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.65	96.49	0.90	0.88	4	-
GCF_016100975.1	s__Lactobacillus sp016100975	89.2999	326	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000760615.1	s__Lactobacillus sp000760615	88.3367	328	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.94	96.94	0.89	0.89	2	-
GCF_013346935.1	s__Lactobacillus melliventris	84.5818	304	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
GCF_900112665.1	s__Lactobacillus bombicola	78.0791	128	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.76	97.11	0.90	0.87	11	-
GCF_001436775.1	s__Lactobacillus acetotolerans	77.1165	88	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.88	98.02	0.91	0.85	26	-
GCF_000296835.1	s__Lactobacillus hominis	76.7701	60	431	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-30 08:37:28,345] [INFO] GTDB search result was written to GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 08:37:28,346] [INFO] ===== GTDB Search completed =====
[2023-06-30 08:37:28,350] [INFO] DFAST_QC result json was written to GCA_946477855.1_SRR7287221_bin.12_metawrap_v1.3.0_MAG_genomic.fna/dqc_result.json
[2023-06-30 08:37:28,350] [INFO] DFAST_QC completed!
[2023-06-30 08:37:28,350] [INFO] Total running time: 0h0m32s