[2023-06-17 07:12:22,858] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:12:22,861] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:12:22,861] [INFO] DQC Reference Directory: /var/lib/cwl/stgad8fff46-beaa-4f05-845d-150725d3a1fb/dqc_reference
[2023-06-17 07:12:25,177] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:12:25,179] [INFO] Task started: Prodigal
[2023-06-17 07:12:25,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg8dd08bb4-d433-45bb-9919-5e76bc63874d/GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna.gz | prodigal -d GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/cds.fna -a GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:12:30,881] [INFO] Task succeeded: Prodigal
[2023-06-17 07:12:30,882] [INFO] Task started: HMMsearch
[2023-06-17 07:12:30,882] [INFO] Running command: hmmsearch --tblout GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad8fff46-beaa-4f05-845d-150725d3a1fb/dqc_reference/reference_markers.hmm GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:12:31,167] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:12:31,169] [INFO] Found 6/6 markers.
[2023-06-17 07:12:31,197] [INFO] Query marker FASTA was written to GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/markers.fasta
[2023-06-17 07:12:31,197] [INFO] Task started: Blastn
[2023-06-17 07:12:31,197] [INFO] Running command: blastn -query GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/markers.fasta -db /var/lib/cwl/stgad8fff46-beaa-4f05-845d-150725d3a1fb/dqc_reference/reference_markers.fasta -out GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:12:31,924] [INFO] Task succeeded: Blastn
[2023-06-17 07:12:31,928] [INFO] Selected 26 target genomes.
[2023-06-17 07:12:31,929] [INFO] Target genome list was writen to GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/target_genomes.txt
[2023-06-17 07:12:31,935] [INFO] Task started: fastANI
[2023-06-17 07:12:31,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dd08bb4-d433-45bb-9919-5e76bc63874d/GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna.gz --refList GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/target_genomes.txt --output GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:12:47,923] [INFO] Task succeeded: fastANI
[2023-06-17 07:12:47,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad8fff46-beaa-4f05-845d-150725d3a1fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:12:47,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad8fff46-beaa-4f05-845d-150725d3a1fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:12:47,936] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 07:12:47,936] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 07:12:47,936] [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
Negativibacillus massiliensis	strain=Marseille-P3213	GCA_900148495.1	1871035	1871035	type	True	78.2778	208	647	95	below_threshold
Provencibacterium massiliense	strain=Marseille-P2780	GCA_900169495.1	1841868	1841868	type	True	76.9738	92	647	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	76.7922	90	647	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.6474	111	647	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	76.6371	78	647	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	76.5084	76	647	95	below_threshold
Angelakisella massiliensis	strain=Marseille-P3217	GCA_900104675.1	1871018	1871018	type	True	76.2387	57	647	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	75.705	59	647	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:12:47,938] [INFO] DFAST Taxonomy check result was written to GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/tc_result.tsv
[2023-06-17 07:12:47,939] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:12:47,939] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:12:47,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad8fff46-beaa-4f05-845d-150725d3a1fb/dqc_reference/checkm_data
[2023-06-17 07:12:47,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:12:47,973] [INFO] Task started: CheckM
[2023-06-17 07:12:47,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/checkm_input GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/checkm_result
[2023-06-17 07:13:11,475] [INFO] Task succeeded: CheckM
[2023-06-17 07:13:11,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.25%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 07:13:11,502] [INFO] ===== Completeness check finished =====
[2023-06-17 07:13:11,502] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:13:11,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/markers.fasta)
[2023-06-17 07:13:11,503] [INFO] Task started: Blastn
[2023-06-17 07:13:11,503] [INFO] Running command: blastn -query GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/markers.fasta -db /var/lib/cwl/stgad8fff46-beaa-4f05-845d-150725d3a1fb/dqc_reference/reference_markers_gtdb.fasta -out GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:13:12,794] [INFO] Task succeeded: Blastn
[2023-06-17 07:13:12,822] [INFO] Selected 16 target genomes.
[2023-06-17 07:13:12,823] [INFO] Target genome list was writen to GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:13:12,833] [INFO] Task started: fastANI
[2023-06-17 07:13:12,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg8dd08bb4-d433-45bb-9919-5e76bc63874d/GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna.gz --refList GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/target_genomes_gtdb.txt --output GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:13:20,117] [INFO] Task succeeded: fastANI
[2023-06-17 07:13:20,132] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 07:13:20,133] [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_900547455.1	s__Negativibacillus faecipullorum	97.6025	595	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.80	97.60	0.92	0.88	7	conclusive
GCA_000435195.1	s__Negativibacillus sp000435195	80.4056	322	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	98.99	98.94	0.90	0.88	5	-
GCA_900547015.1	s__Negativibacillus sp900547015	79.1327	235	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.91	97.91	0.85	0.85	2	-
GCF_900148495.1	s__Negativibacillus massiliensis	78.277	208	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	97.84	97.23	0.93	0.91	5	-
GCA_905197685.1	s__Negativibacillus sp905197685	77.9792	176	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Negativibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904398325.1	s__Neoruminococcus faecicola	76.9413	84	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Neoruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004340125.1	s__Harryflintia acetispora	76.8961	83	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Harryflintia	95.0	98.73	98.54	0.92	0.90	6	-
GCA_014384885.1	s__Hydrogenoanaerobacterium sp014384885	76.8166	89	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	98.59	98.59	0.91	0.91	2	-
GCF_904419105.1	s__Avimicrobium faecavium	76.244	67	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104675.1	s__Angelakisella massiliensis	76.2387	57	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904387055.1	s__Heteroruminococcus faecigallinarum	76.177	71	647	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Heteroruminococcus	95.0	99.97	99.97	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-06-17 07:13:20,135] [INFO] GTDB search result was written to GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/result_gtdb.tsv
[2023-06-17 07:13:20,135] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:13:20,139] [INFO] DFAST_QC result json was written to GCA_905209965.1_ERR260134-mag-bin.53_genomic.fna/dqc_result.json
[2023-06-17 07:13:20,139] [INFO] DFAST_QC completed!
[2023-06-17 07:13:20,139] [INFO] Total running time: 0h0m57s