[2023-06-13 21:21:03,156] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:21:03,158] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:21:03,158] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f8ec2f4-31c5-407b-baf7-f7ecaa7da6fa/dqc_reference
[2023-06-13 21:21:04,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:21:04,412] [INFO] Task started: Prodigal
[2023-06-13 21:21:04,412] [INFO] Running command: gunzip -c /var/lib/cwl/stge85904c1-e1a3-4f2f-af18-e2fd93fb7c16/GCA_022797855.1_ASM2279785v1_genomic.fna.gz | prodigal -d GCA_022797855.1_ASM2279785v1_genomic.fna/cds.fna -a GCA_022797855.1_ASM2279785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:21:11,063] [INFO] Task succeeded: Prodigal
[2023-06-13 21:21:11,063] [INFO] Task started: HMMsearch
[2023-06-13 21:21:11,063] [INFO] Running command: hmmsearch --tblout GCA_022797855.1_ASM2279785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f8ec2f4-31c5-407b-baf7-f7ecaa7da6fa/dqc_reference/reference_markers.hmm GCA_022797855.1_ASM2279785v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:21:11,306] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:21:11,309] [INFO] Found 6/6 markers.
[2023-06-13 21:21:11,337] [INFO] Query marker FASTA was written to GCA_022797855.1_ASM2279785v1_genomic.fna/markers.fasta
[2023-06-13 21:21:11,337] [INFO] Task started: Blastn
[2023-06-13 21:21:11,337] [INFO] Running command: blastn -query GCA_022797855.1_ASM2279785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f8ec2f4-31c5-407b-baf7-f7ecaa7da6fa/dqc_reference/reference_markers.fasta -out GCA_022797855.1_ASM2279785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:11,886] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:11,895] [INFO] Selected 25 target genomes.
[2023-06-13 21:21:11,896] [INFO] Target genome list was writen to GCA_022797855.1_ASM2279785v1_genomic.fna/target_genomes.txt
[2023-06-13 21:21:11,897] [INFO] Task started: fastANI
[2023-06-13 21:21:11,897] [INFO] Running command: fastANI --query /var/lib/cwl/stge85904c1-e1a3-4f2f-af18-e2fd93fb7c16/GCA_022797855.1_ASM2279785v1_genomic.fna.gz --refList GCA_022797855.1_ASM2279785v1_genomic.fna/target_genomes.txt --output GCA_022797855.1_ASM2279785v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:21:23,991] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:23,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f8ec2f4-31c5-407b-baf7-f7ecaa7da6fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:21:23,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f8ec2f4-31c5-407b-baf7-f7ecaa7da6fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:21:23,998] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:21:23,998] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 21:21:23,998] [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
Eubacterium ventriosum	strain=ATCC 27560	GCA_000153885.1	39496	39496	suspected-type	True	78.8348	197	1080	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	78.7355	199	1080	95	below_threshold
Eubacterium uniforme	strain=ATCC 35992	GCA_900167115.1	39495	39495	type	True	77.5327	63	1080	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.0871	54	1080	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	76.8744	51	1080	95	below_threshold
Anaerostipes faecalis	strain=AGMB03513	GCA_018982945.1	2738446	2738446	type	True	76.699	52	1080	95	below_threshold
Velocimicrobium porci	strain=WCA-693-APC-MOT-I	GCA_009696045.1	2606634	2606634	type	True	76.5318	50	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 21:21:24,001] [INFO] DFAST Taxonomy check result was written to GCA_022797855.1_ASM2279785v1_genomic.fna/tc_result.tsv
[2023-06-13 21:21:24,001] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:21:24,001] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:21:24,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f8ec2f4-31c5-407b-baf7-f7ecaa7da6fa/dqc_reference/checkm_data
[2023-06-13 21:21:24,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:21:24,037] [INFO] Task started: CheckM
[2023-06-13 21:21:24,037] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022797855.1_ASM2279785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022797855.1_ASM2279785v1_genomic.fna/checkm_input GCA_022797855.1_ASM2279785v1_genomic.fna/checkm_result
[2023-06-13 21:21:49,785] [INFO] Task succeeded: CheckM
[2023-06-13 21:21:49,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 7.99%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:21:49,811] [INFO] ===== Completeness check finished =====
[2023-06-13 21:21:49,811] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:21:49,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022797855.1_ASM2279785v1_genomic.fna/markers.fasta)
[2023-06-13 21:21:49,811] [INFO] Task started: Blastn
[2023-06-13 21:21:49,812] [INFO] Running command: blastn -query GCA_022797855.1_ASM2279785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f8ec2f4-31c5-407b-baf7-f7ecaa7da6fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_022797855.1_ASM2279785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:50,563] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:50,567] [INFO] Selected 16 target genomes.
[2023-06-13 21:21:50,567] [INFO] Target genome list was writen to GCA_022797855.1_ASM2279785v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:21:50,570] [INFO] Task started: fastANI
[2023-06-13 21:21:50,570] [INFO] Running command: fastANI --query /var/lib/cwl/stge85904c1-e1a3-4f2f-af18-e2fd93fb7c16/GCA_022797855.1_ASM2279785v1_genomic.fna.gz --refList GCA_022797855.1_ASM2279785v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022797855.1_ASM2279785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:21:59,127] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:59,136] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 21:21:59,136] [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
GCA_910584795.1	s__Eubacterium_G sp910584795	99.5293	732	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910574895.1	s__Eubacterium_G sp910574895	90.6324	649	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578975.1	s__Eubacterium_G sp910578975	89.0121	602	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420085.1	s__Eubacterium_G sp904420085	79.4612	326	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003460505.1	s__Eubacterium_G sp000435815	79.3839	263	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.79	97.65	0.84	0.54	8	-
GCA_900550135.1	s__Eubacterium_G sp900550135	79.1343	237	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.87	97.32	0.76	0.74	4	-
GCA_900548465.1	s__Eubacterium_G sp900548465	79.0262	235	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	97.75	97.64	0.80	0.72	3	-
GCF_003479405.1	s__Eubacterium_G sp000432355	78.9901	210	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	99.22	97.56	0.94	0.86	9	-
GCF_000153885.1	s__Eubacterium_G ventriosum	78.8348	197	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_G	95.0	98.27	97.67	0.81	0.64	20	-
GCA_000403295.2	s__Schaedlerella sp000403295	78.4187	56	1080	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.10	98.10	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-13 21:21:59,138] [INFO] GTDB search result was written to GCA_022797855.1_ASM2279785v1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:21:59,139] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:21:59,142] [INFO] DFAST_QC result json was written to GCA_022797855.1_ASM2279785v1_genomic.fna/dqc_result.json
[2023-06-13 21:21:59,142] [INFO] DFAST_QC completed!
[2023-06-13 21:21:59,142] [INFO] Total running time: 0h0m56s