[2023-06-18 21:39:25,571] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:39:25,573] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:39:25,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg93a32e90-6484-4b5c-909a-c886ea735c72/dqc_reference
[2023-06-18 21:39:26,823] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:39:26,824] [INFO] Task started: Prodigal
[2023-06-18 21:39:26,825] [INFO] Running command: gunzip -c /var/lib/cwl/stg35729aa9-7752-4fb8-a11b-7622e6c593fc/GCA_018716285.1_ASM1871628v1_genomic.fna.gz | prodigal -d GCA_018716285.1_ASM1871628v1_genomic.fna/cds.fna -a GCA_018716285.1_ASM1871628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:39:33,462] [INFO] Task succeeded: Prodigal
[2023-06-18 21:39:33,462] [INFO] Task started: HMMsearch
[2023-06-18 21:39:33,462] [INFO] Running command: hmmsearch --tblout GCA_018716285.1_ASM1871628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg93a32e90-6484-4b5c-909a-c886ea735c72/dqc_reference/reference_markers.hmm GCA_018716285.1_ASM1871628v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:39:33,744] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:39:33,746] [INFO] Found 6/6 markers.
[2023-06-18 21:39:33,794] [INFO] Query marker FASTA was written to GCA_018716285.1_ASM1871628v1_genomic.fna/markers.fasta
[2023-06-18 21:39:33,795] [INFO] Task started: Blastn
[2023-06-18 21:39:33,795] [INFO] Running command: blastn -query GCA_018716285.1_ASM1871628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93a32e90-6484-4b5c-909a-c886ea735c72/dqc_reference/reference_markers.fasta -out GCA_018716285.1_ASM1871628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:34,558] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:34,567] [INFO] Selected 26 target genomes.
[2023-06-18 21:39:34,568] [INFO] Target genome list was writen to GCA_018716285.1_ASM1871628v1_genomic.fna/target_genomes.txt
[2023-06-18 21:39:34,571] [INFO] Task started: fastANI
[2023-06-18 21:39:34,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg35729aa9-7752-4fb8-a11b-7622e6c593fc/GCA_018716285.1_ASM1871628v1_genomic.fna.gz --refList GCA_018716285.1_ASM1871628v1_genomic.fna/target_genomes.txt --output GCA_018716285.1_ASM1871628v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:39:50,800] [INFO] Task succeeded: fastANI
[2023-06-18 21:39:50,801] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg93a32e90-6484-4b5c-909a-c886ea735c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:39:50,801] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg93a32e90-6484-4b5c-909a-c886ea735c72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:39:50,810] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:39:50,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 21:39:50,811] [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
Provencibacterium massiliense	strain=Marseille-P2780	GCA_900169495.1	1841868	1841868	type	True	76.9293	114	857	95	below_threshold
Fumia xinanensis	strain=NSJ-33	GCA_014384905.1	2763659	2763659	type	True	76.7018	90	857	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	76.6096	64	857	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.5333	55	857	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.5085	77	857	95	below_threshold
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	76.4741	60	857	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	76.4214	53	857	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	76.2596	70	857	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	75.9586	52	857	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 21:39:50,814] [INFO] DFAST Taxonomy check result was written to GCA_018716285.1_ASM1871628v1_genomic.fna/tc_result.tsv
[2023-06-18 21:39:50,815] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:39:50,815] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:39:50,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg93a32e90-6484-4b5c-909a-c886ea735c72/dqc_reference/checkm_data
[2023-06-18 21:39:50,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:39:50,845] [INFO] Task started: CheckM
[2023-06-18 21:39:50,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018716285.1_ASM1871628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018716285.1_ASM1871628v1_genomic.fna/checkm_input GCA_018716285.1_ASM1871628v1_genomic.fna/checkm_result
[2023-06-18 21:40:16,486] [INFO] Task succeeded: CheckM
[2023-06-18 21:40:16,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:40:16,520] [INFO] ===== Completeness check finished =====
[2023-06-18 21:40:16,520] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:40:16,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018716285.1_ASM1871628v1_genomic.fna/markers.fasta)
[2023-06-18 21:40:16,522] [INFO] Task started: Blastn
[2023-06-18 21:40:16,522] [INFO] Running command: blastn -query GCA_018716285.1_ASM1871628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg93a32e90-6484-4b5c-909a-c886ea735c72/dqc_reference/reference_markers_gtdb.fasta -out GCA_018716285.1_ASM1871628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:40:17,862] [INFO] Task succeeded: Blastn
[2023-06-18 21:40:17,867] [INFO] Selected 12 target genomes.
[2023-06-18 21:40:17,867] [INFO] Target genome list was writen to GCA_018716285.1_ASM1871628v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:40:17,872] [INFO] Task started: fastANI
[2023-06-18 21:40:17,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg35729aa9-7752-4fb8-a11b-7622e6c593fc/GCA_018716285.1_ASM1871628v1_genomic.fna.gz --refList GCA_018716285.1_ASM1871628v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018716285.1_ASM1871628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:40:23,883] [INFO] Task succeeded: fastANI
[2023-06-18 21:40:23,894] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:40:23,894] [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_018716285.1	s__Merdivicinus faecavium	100.0	853	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	99.37	98.77	0.95	0.93	3	conclusive
GCA_018713245.1	s__Merdivicinus intestinavium	80.6238	368	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	99.92	99.92	0.95	0.95	2	-
GCA_018713335.1	s__Merdivicinus intestinigallinarum	80.0506	357	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018716725.1	s__Merdivicinus excrementipullorum	79.8307	314	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	99.35	99.04	0.91	0.87	4	-
GCA_018712425.1	s__Faecivivens stercoravium	78.3503	137	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecivivens	95.0	97.86	97.02	0.86	0.77	8	-
GCA_900555435.1	s__Merdivicinus sp900555435	78.2991	170	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	98.51	98.40	0.89	0.88	3	-
GCA_905214265.1	s__Merdivicinus sp905214265	77.9328	219	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Merdivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760305.1	s__UMGS856 sp900760305	76.6302	67	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS856	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553255.1	s__UMGS1591 sp900553255	76.4207	58	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS1591	95.0	100.00	100.00	0.98	0.98	2	-
GCF_904419005.1	s__Avimonas faecium	76.3538	82	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	99.95	99.95	0.90	0.90	2	-
GCA_905198155.1	s__RGIG4076 sp905198155	75.7172	51	857	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__RGIG4076	95.0	98.68	98.68	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-06-18 21:40:23,896] [INFO] GTDB search result was written to GCA_018716285.1_ASM1871628v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:40:23,897] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:40:23,904] [INFO] DFAST_QC result json was written to GCA_018716285.1_ASM1871628v1_genomic.fna/dqc_result.json
[2023-06-18 21:40:23,905] [INFO] DFAST_QC completed!
[2023-06-18 21:40:23,905] [INFO] Total running time: 0h0m58s