[2024-01-24 12:07:06,820] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg697c7cd1-6159-4839-a5bf-ca6ce103a93d/dqc_reference
[2024-01-24 12:07:08,046] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:08,047] [INFO] Task started: Prodigal
[2024-01-24 12:07:08,047] [INFO] Running command: gunzip -c /var/lib/cwl/stg5218af31-671b-4258-a8a5-5180f2835d80/GCF_014281125.1_ASM1428112v1_genomic.fna.gz | prodigal -d GCF_014281125.1_ASM1428112v1_genomic.fna/cds.fna -a GCF_014281125.1_ASM1428112v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:15,823] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:15,824] [INFO] Task started: HMMsearch
[2024-01-24 12:07:15,824] [INFO] Running command: hmmsearch --tblout GCF_014281125.1_ASM1428112v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg697c7cd1-6159-4839-a5bf-ca6ce103a93d/dqc_reference/reference_markers.hmm GCF_014281125.1_ASM1428112v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:16,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:16,084] [INFO] Found 6/6 markers.
[2024-01-24 12:07:16,111] [INFO] Query marker FASTA was written to GCF_014281125.1_ASM1428112v1_genomic.fna/markers.fasta
[2024-01-24 12:07:16,111] [INFO] Task started: Blastn
[2024-01-24 12:07:16,111] [INFO] Running command: blastn -query GCF_014281125.1_ASM1428112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg697c7cd1-6159-4839-a5bf-ca6ce103a93d/dqc_reference/reference_markers.fasta -out GCF_014281125.1_ASM1428112v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:16,773] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:16,776] [INFO] Selected 10 target genomes.
[2024-01-24 12:07:16,776] [INFO] Target genome list was writen to GCF_014281125.1_ASM1428112v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:16,778] [INFO] Task started: fastANI
[2024-01-24 12:07:16,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg5218af31-671b-4258-a8a5-5180f2835d80/GCF_014281125.1_ASM1428112v1_genomic.fna.gz --refList GCF_014281125.1_ASM1428112v1_genomic.fna/target_genomes.txt --output GCF_014281125.1_ASM1428112v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:22,143] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:22,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg697c7cd1-6159-4839-a5bf-ca6ce103a93d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:22,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg697c7cd1-6159-4839-a5bf-ca6ce103a93d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:22,162] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:22,163] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:22,163] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	81.0183	452	867	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	80.9832	413	867	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	79.7162	349	867	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.0688	242	867	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	79.0278	290	867	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	78.9702	275	867	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	78.9552	293	867	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.2676	198	867	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	78.0387	134	867	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.9106	161	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:22,164] [INFO] DFAST Taxonomy check result was written to GCF_014281125.1_ASM1428112v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:22,165] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:22,165] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:22,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg697c7cd1-6159-4839-a5bf-ca6ce103a93d/dqc_reference/checkm_data
[2024-01-24 12:07:22,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:22,201] [INFO] Task started: CheckM
[2024-01-24 12:07:22,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014281125.1_ASM1428112v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014281125.1_ASM1428112v1_genomic.fna/checkm_input GCF_014281125.1_ASM1428112v1_genomic.fna/checkm_result
[2024-01-24 12:07:50,191] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:50,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:50,217] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:50,217] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:50,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014281125.1_ASM1428112v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:50,218] [INFO] Task started: Blastn
[2024-01-24 12:07:50,218] [INFO] Running command: blastn -query GCF_014281125.1_ASM1428112v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg697c7cd1-6159-4839-a5bf-ca6ce103a93d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014281125.1_ASM1428112v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:51,436] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:51,440] [INFO] Selected 20 target genomes.
[2024-01-24 12:07:51,440] [INFO] Target genome list was writen to GCF_014281125.1_ASM1428112v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:51,463] [INFO] Task started: fastANI
[2024-01-24 12:07:51,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg5218af31-671b-4258-a8a5-5180f2835d80/GCF_014281125.1_ASM1428112v1_genomic.fna.gz --refList GCF_014281125.1_ASM1428112v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014281125.1_ASM1428112v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:03,370] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:03,390] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:03,391] [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_014281125.1	s__Instestinimonas_A gabonensis	100.0	867	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Instestinimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002161215.1	s__Flavonifractor avistercoris	81.4919	453	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_002159455.1	s__Flavonifractor sp002159455	81.2504	403	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	97.17	96.82	0.76	0.75	4	-
GCF_000239295.1	s__Flavonifractor plautii	81.024	410	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.23	97.77	0.83	0.59	43	-
GCA_900549565.1	s__UMGS1202 sp900549565	80.6663	391	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159265.1	s__Flavonifractor sp002159265	80.6652	405	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017811815.1	s__Flavonifractor sp017811815	80.6646	383	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002161085.1	s__Flavonifractor avicola	80.5072	373	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.94	96.68	0.83	0.78	7	-
GCA_904419835.1	s__Pseudoflavonifractor sp904419835	80.3837	322	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901955.1	s__Flavonifractor phocaeensis_A	80.3694	346	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287895.1	s__NSJ-51 sp900549795	80.344	418	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	99.27	99.06	0.90	0.89	3	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	80.2633	331	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
GCF_000169255.2	s__Pseudoflavonifractor capillosus	79.9229	371	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	95.82	95.81	0.78	0.78	3	-
GCF_900199495.1	s__An92 sp900199495	79.7558	335	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	-
GCA_018374635.1	s__An92 sp018374635	79.4879	312	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287875.1	s__Lawsonibacter sp014287875	79.3789	241	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.47	96.91	0.89	0.83	4	-
GCA_019117605.1	s__Intestinimonas stercoravium	79.3549	283	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.97	98.96	0.85	0.84	3	-
GCA_910585155.1	s__Enterenecus sp910585155	78.7826	216	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Enterenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334055.1	s__NSJ-62 sp014334055	78.6823	160	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-62	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373635.1	s__Pelethomonas sp902373635	78.3698	176	867	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:03,392] [INFO] GTDB search result was written to GCF_014281125.1_ASM1428112v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:03,393] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:03,397] [INFO] DFAST_QC result json was written to GCF_014281125.1_ASM1428112v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:03,397] [INFO] DFAST_QC completed!
[2024-01-24 12:08:03,397] [INFO] Total running time: 0h0m57s