[2023-06-17 12:04:43,566] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:04:43,574] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:04:43,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f39b6c0-bf48-4319-8a94-bde5d1512af6/dqc_reference
[2023-06-17 12:04:45,840] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:04:45,841] [INFO] Task started: Prodigal
[2023-06-17 12:04:45,842] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb723b11-22ae-471f-bfff-39a1b0e3f313/GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna.gz | prodigal -d GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/cds.fna -a GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:04:51,421] [INFO] Task succeeded: Prodigal
[2023-06-17 12:04:51,421] [INFO] Task started: HMMsearch
[2023-06-17 12:04:51,422] [INFO] Running command: hmmsearch --tblout GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f39b6c0-bf48-4319-8a94-bde5d1512af6/dqc_reference/reference_markers.hmm GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:04:51,684] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:04:51,686] [INFO] Found 6/6 markers.
[2023-06-17 12:04:51,714] [INFO] Query marker FASTA was written to GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/markers.fasta
[2023-06-17 12:04:51,715] [INFO] Task started: Blastn
[2023-06-17 12:04:51,715] [INFO] Running command: blastn -query GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f39b6c0-bf48-4319-8a94-bde5d1512af6/dqc_reference/reference_markers.fasta -out GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:04:52,349] [INFO] Task succeeded: Blastn
[2023-06-17 12:04:52,354] [INFO] Selected 14 target genomes.
[2023-06-17 12:04:52,354] [INFO] Target genome list was writen to GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/target_genomes.txt
[2023-06-17 12:04:52,357] [INFO] Task started: fastANI
[2023-06-17 12:04:52,357] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb723b11-22ae-471f-bfff-39a1b0e3f313/GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna.gz --refList GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/target_genomes.txt --output GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:05:01,424] [INFO] Task succeeded: fastANI
[2023-06-17 12:05:01,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f39b6c0-bf48-4319-8a94-bde5d1512af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:05:01,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f39b6c0-bf48-4319-8a94-bde5d1512af6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:05:01,445] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2023-06-17 12:05:01,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 12:05:01,446] [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 hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	97.8056	722	834	95	conclusive
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	97.7507	728	834	95	conclusive
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	97.7503	724	834	95	conclusive
Blautia argi	strain=KCTC 15426	GCA_003287895.1	1912897	1912897	type	True	80.0863	376	834	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.7876	102	834	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.9412	97	834	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	77.7486	146	834	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.6138	91	834	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	77.5854	149	834	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.5572	160	834	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.4917	168	834	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.4508	166	834	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	75.7888	63	834	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:05:01,448] [INFO] DFAST Taxonomy check result was written to GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/tc_result.tsv
[2023-06-17 12:05:01,449] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:05:01,450] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:05:01,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f39b6c0-bf48-4319-8a94-bde5d1512af6/dqc_reference/checkm_data
[2023-06-17 12:05:01,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:05:01,485] [INFO] Task started: CheckM
[2023-06-17 12:05:01,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/checkm_input GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/checkm_result
[2023-06-17 12:05:24,538] [INFO] Task succeeded: CheckM
[2023-06-17 12:05:24,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:05:24,570] [INFO] ===== Completeness check finished =====
[2023-06-17 12:05:24,571] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:05:24,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/markers.fasta)
[2023-06-17 12:05:24,573] [INFO] Task started: Blastn
[2023-06-17 12:05:24,573] [INFO] Running command: blastn -query GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f39b6c0-bf48-4319-8a94-bde5d1512af6/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:05:25,609] [INFO] Task succeeded: Blastn
[2023-06-17 12:05:25,613] [INFO] Selected 6 target genomes.
[2023-06-17 12:05:25,613] [INFO] Target genome list was writen to GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:05:25,620] [INFO] Task started: fastANI
[2023-06-17 12:05:25,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb723b11-22ae-471f-bfff-39a1b0e3f313/GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna.gz --refList GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/target_genomes_gtdb.txt --output GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:05:29,700] [INFO] Task succeeded: fastANI
[2023-06-17 12:05:29,708] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:05:29,708] [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_002222595.2	s__Blautia hansenii	97.7503	724	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.38	97.55	0.86	0.75	11	conclusive
GCA_900539145.1	s__Blautia sp900539145	94.5536	687	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.09	98.22	0.85	0.80	3	-
GCA_905201915.1	s__Blautia sp900555025	91.063	593	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.26	99.26	0.76	0.76	2	-
GCF_900120295.1	s__Blautia sp900120295	89.6537	680	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547685.1	s__Blautia sp900547685	88.9726	572	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013304445.1	s__Blautia sp900541955	79.6694	367	834	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.45	99.32	0.89	0.85	6	-
--------------------------------------------------------------------------------
[2023-06-17 12:05:29,710] [INFO] GTDB search result was written to GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/result_gtdb.tsv
[2023-06-17 12:05:29,711] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:05:29,714] [INFO] DFAST_QC result json was written to GCA_905201995.1_ERR1190584-mag-bin.22_genomic.fna/dqc_result.json
[2023-06-17 12:05:29,715] [INFO] DFAST_QC completed!
[2023-06-17 12:05:29,715] [INFO] Total running time: 0h0m46s