[2023-06-19 08:40:18,993] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:40:18,996] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:40:18,996] [INFO] DQC Reference Directory: /var/lib/cwl/stg68cce80a-47c8-47de-9e32-717da0749426/dqc_reference
[2023-06-19 08:40:20,273] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:40:20,273] [INFO] Task started: Prodigal
[2023-06-19 08:40:20,274] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b412244-15b2-43f3-a181-97609c9a9357/GCA_018054285.1_ASM1805428v1_genomic.fna.gz | prodigal -d GCA_018054285.1_ASM1805428v1_genomic.fna/cds.fna -a GCA_018054285.1_ASM1805428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:40:22,796] [INFO] Task succeeded: Prodigal
[2023-06-19 08:40:22,797] [INFO] Task started: HMMsearch
[2023-06-19 08:40:22,797] [INFO] Running command: hmmsearch --tblout GCA_018054285.1_ASM1805428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68cce80a-47c8-47de-9e32-717da0749426/dqc_reference/reference_markers.hmm GCA_018054285.1_ASM1805428v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:40:23,018] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:40:23,021] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8b412244-15b2-43f3-a181-97609c9a9357/GCA_018054285.1_ASM1805428v1_genomic.fna.gz]
[2023-06-19 08:40:23,042] [INFO] Query marker FASTA was written to GCA_018054285.1_ASM1805428v1_genomic.fna/markers.fasta
[2023-06-19 08:40:23,043] [INFO] Task started: Blastn
[2023-06-19 08:40:23,043] [INFO] Running command: blastn -query GCA_018054285.1_ASM1805428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68cce80a-47c8-47de-9e32-717da0749426/dqc_reference/reference_markers.fasta -out GCA_018054285.1_ASM1805428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:23,574] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:23,579] [INFO] Selected 11 target genomes.
[2023-06-19 08:40:23,580] [INFO] Target genome list was writen to GCA_018054285.1_ASM1805428v1_genomic.fna/target_genomes.txt
[2023-06-19 08:40:23,581] [INFO] Task started: fastANI
[2023-06-19 08:40:23,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b412244-15b2-43f3-a181-97609c9a9357/GCA_018054285.1_ASM1805428v1_genomic.fna.gz --refList GCA_018054285.1_ASM1805428v1_genomic.fna/target_genomes.txt --output GCA_018054285.1_ASM1805428v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:40:30,471] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:30,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68cce80a-47c8-47de-9e32-717da0749426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:40:30,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68cce80a-47c8-47de-9e32-717da0749426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:40:30,484] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:40:30,484] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:40:30,484] [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
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.3565	112	300	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.2015	112	300	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.1974	111	300	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	79.0355	95	300	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.9888	98	300	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.7539	84	300	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	78.6263	105	300	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.0446	84	300	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:40:30,487] [INFO] DFAST Taxonomy check result was written to GCA_018054285.1_ASM1805428v1_genomic.fna/tc_result.tsv
[2023-06-19 08:40:30,487] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:40:30,488] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:40:30,488] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68cce80a-47c8-47de-9e32-717da0749426/dqc_reference/checkm_data
[2023-06-19 08:40:30,489] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:40:30,514] [INFO] Task started: CheckM
[2023-06-19 08:40:30,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018054285.1_ASM1805428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018054285.1_ASM1805428v1_genomic.fna/checkm_input GCA_018054285.1_ASM1805428v1_genomic.fna/checkm_result
[2023-06-19 08:40:45,855] [INFO] Task succeeded: CheckM
[2023-06-19 08:40:45,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:40:45,880] [INFO] ===== Completeness check finished =====
[2023-06-19 08:40:45,880] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:40:45,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018054285.1_ASM1805428v1_genomic.fna/markers.fasta)
[2023-06-19 08:40:45,881] [INFO] Task started: Blastn
[2023-06-19 08:40:45,881] [INFO] Running command: blastn -query GCA_018054285.1_ASM1805428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68cce80a-47c8-47de-9e32-717da0749426/dqc_reference/reference_markers_gtdb.fasta -out GCA_018054285.1_ASM1805428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:40:46,371] [INFO] Task succeeded: Blastn
[2023-06-19 08:40:46,375] [INFO] Selected 10 target genomes.
[2023-06-19 08:40:46,375] [INFO] Target genome list was writen to GCA_018054285.1_ASM1805428v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:40:46,376] [INFO] Task started: fastANI
[2023-06-19 08:40:46,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b412244-15b2-43f3-a181-97609c9a9357/GCA_018054285.1_ASM1805428v1_genomic.fna.gz --refList GCA_018054285.1_ASM1805428v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018054285.1_ASM1805428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:40:52,092] [INFO] Task succeeded: fastANI
[2023-06-19 08:40:52,108] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:40:52,109] [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_016908695.1	s__Blautia_A faecis	98.3285	278	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.52	97.01	0.80	0.69	30	conclusive
GCA_905206915.1	s__Blautia_A sp905206915	87.0345	199	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003460605.1	s__Blautia_A sp900066145	84.2231	234	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.04	98.72	0.92	0.85	9	-
GCA_900763175.1	s__Blautia_A sp900763175	82.7732	188	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153905.1	s__Blautia_A obeum	79.0355	95	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.25	97.20	0.82	0.75	45	-
GCA_900316115.1	s__Blautia_A sp900316115	78.865	103	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.53	99.48	0.92	0.90	3	-
GCF_013304735.1	s__Blautia_A sp900066205	78.7236	100	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCF_003461955.1	s__Blautia_A sp900066335	78.6416	109	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.25	0.89	0.82	13	-
GCA_900764225.1	s__Blautia_A sp900764225	78.6288	77	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003477525.1	s__Blautia_A sp003477525	78.603	99	300	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.30	98.60	0.90	0.81	3	-
--------------------------------------------------------------------------------
[2023-06-19 08:40:52,113] [INFO] GTDB search result was written to GCA_018054285.1_ASM1805428v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:40:52,113] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:40:52,117] [INFO] DFAST_QC result json was written to GCA_018054285.1_ASM1805428v1_genomic.fna/dqc_result.json
[2023-06-19 08:40:52,118] [INFO] DFAST_QC completed!
[2023-06-19 08:40:52,118] [INFO] Total running time: 0h0m33s