[2023-06-18 11:44:48,675] [INFO] DFAST_QC pipeline started.
[2023-06-18 11:44:48,678] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 11:44:48,678] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b74634b-d800-4f52-ac8d-39396872cc3e/dqc_reference
[2023-06-18 11:44:49,950] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 11:44:49,951] [INFO] Task started: Prodigal
[2023-06-18 11:44:49,952] [INFO] Running command: gunzip -c /var/lib/cwl/stg4492ef58-d6a4-41cd-a516-c492fb682eb4/GCA_018264995.1_ASM1826499v1_genomic.fna.gz | prodigal -d GCA_018264995.1_ASM1826499v1_genomic.fna/cds.fna -a GCA_018264995.1_ASM1826499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 11:44:54,171] [INFO] Task succeeded: Prodigal
[2023-06-18 11:44:54,171] [INFO] Task started: HMMsearch
[2023-06-18 11:44:54,172] [INFO] Running command: hmmsearch --tblout GCA_018264995.1_ASM1826499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b74634b-d800-4f52-ac8d-39396872cc3e/dqc_reference/reference_markers.hmm GCA_018264995.1_ASM1826499v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 11:44:54,437] [INFO] Task succeeded: HMMsearch
[2023-06-18 11:44:54,438] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4492ef58-d6a4-41cd-a516-c492fb682eb4/GCA_018264995.1_ASM1826499v1_genomic.fna.gz]
[2023-06-18 11:44:54,463] [INFO] Query marker FASTA was written to GCA_018264995.1_ASM1826499v1_genomic.fna/markers.fasta
[2023-06-18 11:44:54,463] [INFO] Task started: Blastn
[2023-06-18 11:44:54,463] [INFO] Running command: blastn -query GCA_018264995.1_ASM1826499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b74634b-d800-4f52-ac8d-39396872cc3e/dqc_reference/reference_markers.fasta -out GCA_018264995.1_ASM1826499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:44:55,072] [INFO] Task succeeded: Blastn
[2023-06-18 11:44:55,077] [INFO] Selected 19 target genomes.
[2023-06-18 11:44:55,077] [INFO] Target genome list was writen to GCA_018264995.1_ASM1826499v1_genomic.fna/target_genomes.txt
[2023-06-18 11:44:55,078] [INFO] Task started: fastANI
[2023-06-18 11:44:55,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg4492ef58-d6a4-41cd-a516-c492fb682eb4/GCA_018264995.1_ASM1826499v1_genomic.fna.gz --refList GCA_018264995.1_ASM1826499v1_genomic.fna/target_genomes.txt --output GCA_018264995.1_ASM1826499v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 11:45:04,284] [INFO] Task succeeded: fastANI
[2023-06-18 11:45:04,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b74634b-d800-4f52-ac8d-39396872cc3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 11:45:04,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b74634b-d800-4f52-ac8d-39396872cc3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 11:45:04,305] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2023-06-18 11:45:04,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 11:45:04,305] [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
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	98.9708	530	569	95	conclusive
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	98.9467	537	569	95	conclusive
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.4955	126	569	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.4736	127	569	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	78.1674	181	569	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	78.1393	184	569	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.9294	160	569	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.6361	120	569	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	77.6354	82	569	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.5604	84	569	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	77.5187	76	569	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.3942	126	569	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.2389	111	569	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.2316	110	569	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.1901	109	569	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.1721	118	569	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.9648	81	569	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	76.9266	93	569	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	76.8875	89	569	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 11:45:04,307] [INFO] DFAST Taxonomy check result was written to GCA_018264995.1_ASM1826499v1_genomic.fna/tc_result.tsv
[2023-06-18 11:45:04,308] [INFO] ===== Taxonomy check completed =====
[2023-06-18 11:45:04,308] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 11:45:04,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b74634b-d800-4f52-ac8d-39396872cc3e/dqc_reference/checkm_data
[2023-06-18 11:45:04,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 11:45:04,340] [INFO] Task started: CheckM
[2023-06-18 11:45:04,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018264995.1_ASM1826499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018264995.1_ASM1826499v1_genomic.fna/checkm_input GCA_018264995.1_ASM1826499v1_genomic.fna/checkm_result
[2023-06-18 11:45:25,005] [INFO] Task succeeded: CheckM
[2023-06-18 11:45:25,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.47%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 11:45:25,026] [INFO] ===== Completeness check finished =====
[2023-06-18 11:45:25,026] [INFO] ===== Start GTDB Search =====
[2023-06-18 11:45:25,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018264995.1_ASM1826499v1_genomic.fna/markers.fasta)
[2023-06-18 11:45:25,027] [INFO] Task started: Blastn
[2023-06-18 11:45:25,027] [INFO] Running command: blastn -query GCA_018264995.1_ASM1826499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b74634b-d800-4f52-ac8d-39396872cc3e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018264995.1_ASM1826499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 11:45:25,880] [INFO] Task succeeded: Blastn
[2023-06-18 11:45:25,885] [INFO] Selected 20 target genomes.
[2023-06-18 11:45:25,885] [INFO] Target genome list was writen to GCA_018264995.1_ASM1826499v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 11:45:25,896] [INFO] Task started: fastANI
[2023-06-18 11:45:25,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg4492ef58-d6a4-41cd-a516-c492fb682eb4/GCA_018264995.1_ASM1826499v1_genomic.fna.gz --refList GCA_018264995.1_ASM1826499v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018264995.1_ASM1826499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 11:45:35,480] [INFO] Task succeeded: fastANI
[2023-06-18 11:45:35,509] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 11:45:35,509] [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_000154065.1	s__Dorea_A longicatena	98.9708	530	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	conclusive
GCF_001404875.1	s__Dorea_A longicatena_B	90.3648	476	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCA_900550865.1	s__Dorea_A sp900550865	89.6273	447	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003435815.1	s__CAG-317 sp000433215	78.7547	215	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCF_000155205.1	s__Mediterraneibacter lactaris	78.4736	127	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCA_016295505.1	s__Dorea_A sp016295505	78.4044	180	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169235.1	s__Dorea formicigenerans	78.1188	185	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	-
GCA_004556565.1	s__Schaedlerella sp004556565	77.7933	64	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300825.1	s__Blautia_A wexlerae_B	77.7389	74	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_003477705.1	s__Lachnoclostridium_B sp900066555	77.7086	150	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	97.98	96.92	0.87	0.81	6	-
GCF_000484655.1	s__Blautia_A wexlerae	77.6353	82	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.38	96.15	0.76	0.65	140	-
GCA_900554415.1	s__Bariatricus sp900554415	77.3399	58	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.94	99.94	0.94	0.94	2	-
GCF_003471165.1	s__Blautia_A sp003471165	77.26	75	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.40	97.74	0.83	0.79	20	-
GCF_008121495.1	s__Ruminococcus_B gnavus	77.2316	110	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCA_905209435.1	s__Blautia_A sp905209435	77.0754	53	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919065.1	s__Blautia_A sp018919065	76.8039	80	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578865.1	s__CAG-317 sp011960265	76.6601	109	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	99.18	99.18	0.88	0.88	2	-
GCA_905209865.1	s__Mediterraneibacter sp900752395	76.6168	52	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	-
GCA_904418845.1	s__Mediterraneibacter sp904418845	76.1502	62	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120275.1	s__Mediterraneibacter excrementavium	76.0685	50	569	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 11:45:35,512] [INFO] GTDB search result was written to GCA_018264995.1_ASM1826499v1_genomic.fna/result_gtdb.tsv
[2023-06-18 11:45:35,512] [INFO] ===== GTDB Search completed =====
[2023-06-18 11:45:35,516] [INFO] DFAST_QC result json was written to GCA_018264995.1_ASM1826499v1_genomic.fna/dqc_result.json
[2023-06-18 11:45:35,517] [INFO] DFAST_QC completed!
[2023-06-18 11:45:35,517] [INFO] Total running time: 0h0m47s