[2023-06-08 14:46:33,143] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:46:33,147] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:46:33,148] [INFO] DQC Reference Directory: /var/lib/cwl/stg2ccde340-1ad0-4642-b092-5b11662bb348/dqc_reference
[2023-06-08 14:46:34,880] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:46:34,882] [INFO] Task started: Prodigal
[2023-06-08 14:46:34,882] [INFO] Running command: gunzip -c /var/lib/cwl/stg8897d72f-e911-46ff-abb1-502e0a28e242/GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna.gz | prodigal -d GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/cds.fna -a GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:46:38,878] [INFO] Task succeeded: Prodigal
[2023-06-08 14:46:38,879] [INFO] Task started: HMMsearch
[2023-06-08 14:46:38,879] [INFO] Running command: hmmsearch --tblout GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2ccde340-1ad0-4642-b092-5b11662bb348/dqc_reference/reference_markers.hmm GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:46:39,176] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:46:39,177] [INFO] Found 6/6 markers.
[2023-06-08 14:46:39,209] [INFO] Query marker FASTA was written to GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta
[2023-06-08 14:46:39,209] [INFO] Task started: Blastn
[2023-06-08 14:46:39,209] [INFO] Running command: blastn -query GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ccde340-1ad0-4642-b092-5b11662bb348/dqc_reference/reference_markers.fasta -out GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:46:39,886] [INFO] Task succeeded: Blastn
[2023-06-08 14:46:39,890] [INFO] Selected 19 target genomes.
[2023-06-08 14:46:39,890] [INFO] Target genome list was writen to GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt
[2023-06-08 14:46:39,892] [INFO] Task started: fastANI
[2023-06-08 14:46:39,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg8897d72f-e911-46ff-abb1-502e0a28e242/GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/target_genomes.txt --output GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:46:45,605] [INFO] Task succeeded: fastANI
[2023-06-08 14:46:45,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2ccde340-1ad0-4642-b092-5b11662bb348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:46:45,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2ccde340-1ad0-4642-b092-5b11662bb348/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:46:45,623] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:46:45,623] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:46:45,623] [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	84.2047	414	654	95	below_threshold
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	83.5434	396	654	95	below_threshold
Lactobacillus apis	strain=CCM 8403	GCA_014635365.1	303541	303541	type	True	78.648	193	654	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.381	177	654	95	below_threshold
Lactobacillus bombicola	strain=R-53102	GCA_900112665.1	1505723	1505723	type	True	77.6191	164	654	95	below_threshold
Lactobacillus bombicola	strain=H70-3	GCA_002916915.1	1505723	1505723	type	True	77.5991	167	654	95	below_threshold
Lactobacillus xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	77.2667	64	654	95	below_threshold
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	77.1226	81	654	95	below_threshold
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	77.1161	83	654	95	below_threshold
Lactobacillus acetotolerans	strain=DSM 20749	GCA_001436775.1	1600	1600	type	True	77.0604	97	654	95	below_threshold
Lactobacillus acetotolerans	strain=JCM 3825	GCA_014648715.1	1600	1600	type	True	76.987	101	654	95	below_threshold
Lactobacillus gigeriorum	strain=DSM 23908	GCA_001436575.1	1203069	1203069	type	True	76.8533	77	654	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	76.8217	68	654	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_004354545.1	83683	83683	type	True	76.8183	72	654	95	below_threshold
Lactobacillus gigeriorum	strain=type strain: CRBIP 24.85	GCA_000296855.1	1203069	1203069	type	True	76.778	80	654	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	76.5537	86	654	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:46:45,626] [INFO] DFAST Taxonomy check result was written to GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/tc_result.tsv
[2023-06-08 14:46:45,626] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:46:45,626] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:46:45,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2ccde340-1ad0-4642-b092-5b11662bb348/dqc_reference/checkm_data
[2023-06-08 14:46:45,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:46:45,651] [INFO] Task started: CheckM
[2023-06-08 14:46:45,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/checkm_input GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/checkm_result
[2023-06-08 14:47:05,138] [INFO] Task succeeded: CheckM
[2023-06-08 14:47:05,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:47:05,158] [INFO] ===== Completeness check finished =====
[2023-06-08 14:47:05,158] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:47:05,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta)
[2023-06-08 14:47:05,159] [INFO] Task started: Blastn
[2023-06-08 14:47:05,159] [INFO] Running command: blastn -query GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2ccde340-1ad0-4642-b092-5b11662bb348/dqc_reference/reference_markers_gtdb.fasta -out GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:47:05,939] [INFO] Task succeeded: Blastn
[2023-06-08 14:47:05,943] [INFO] Selected 8 target genomes.
[2023-06-08 14:47:05,943] [INFO] Target genome list was writen to GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:47:05,944] [INFO] Task started: fastANI
[2023-06-08 14:47:05,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg8897d72f-e911-46ff-abb1-502e0a28e242/GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna.gz --refList GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:47:09,439] [INFO] Task succeeded: fastANI
[2023-06-08 14:47:09,450] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 14:47:09,451] [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_013346935.1	s__Lactobacillus melliventris	94.132	509	654	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
GCF_000970755.1	s__Lactobacillus kimbladii_A	84.1598	431	654	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	84.1149	424	654	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.65	96.49	0.90	0.88	4	-
GCF_014323605.1	s__Lactobacillus kimbladii_B	83.938	401	654	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016100975.1	s__Lactobacillus sp016100975	83.9202	423	654	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	83.5828	403	654	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.94	96.94	0.89	0.89	2	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	83.0835	380	654	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
GCF_002916935.1	s__Lactobacillus panisapium	79.1653	216	654	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 14:47:09,453] [INFO] GTDB search result was written to GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 14:47:09,453] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:47:09,458] [INFO] DFAST_QC result json was written to GCA_945290125.1_SRR11267073_bin.2_metawrap_v1.3.0_MAG_genomic.fna/dqc_result.json
[2023-06-08 14:47:09,458] [INFO] DFAST_QC completed!
[2023-06-08 14:47:09,458] [INFO] Total running time: 0h0m36s