[2024-01-25 20:15:20,709] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:15:20,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:15:20,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg2142dacd-51be-4160-84e9-c3a753abbd9e/dqc_reference
[2024-01-25 20:15:21,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:15:21,853] [INFO] Task started: Prodigal
[2024-01-25 20:15:21,854] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5779bfb-3464-4fdf-b442-d6929348f974/GCF_025566965.1_ASM2556696v1_genomic.fna.gz | prodigal -d GCF_025566965.1_ASM2556696v1_genomic.fna/cds.fna -a GCF_025566965.1_ASM2556696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:30,158] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:30,158] [INFO] Task started: HMMsearch
[2024-01-25 20:15:30,158] [INFO] Running command: hmmsearch --tblout GCF_025566965.1_ASM2556696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2142dacd-51be-4160-84e9-c3a753abbd9e/dqc_reference/reference_markers.hmm GCF_025566965.1_ASM2556696v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:30,409] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:30,410] [INFO] Found 6/6 markers.
[2024-01-25 20:15:30,441] [INFO] Query marker FASTA was written to GCF_025566965.1_ASM2556696v1_genomic.fna/markers.fasta
[2024-01-25 20:15:30,441] [INFO] Task started: Blastn
[2024-01-25 20:15:30,441] [INFO] Running command: blastn -query GCF_025566965.1_ASM2556696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2142dacd-51be-4160-84e9-c3a753abbd9e/dqc_reference/reference_markers.fasta -out GCF_025566965.1_ASM2556696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:31,032] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:31,034] [INFO] Selected 16 target genomes.
[2024-01-25 20:15:31,035] [INFO] Target genome list was writen to GCF_025566965.1_ASM2556696v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:31,040] [INFO] Task started: fastANI
[2024-01-25 20:15:31,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5779bfb-3464-4fdf-b442-d6929348f974/GCF_025566965.1_ASM2556696v1_genomic.fna.gz --refList GCF_025566965.1_ASM2556696v1_genomic.fna/target_genomes.txt --output GCF_025566965.1_ASM2556696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:41,042] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:41,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2142dacd-51be-4160-84e9-c3a753abbd9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:41,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2142dacd-51be-4160-84e9-c3a753abbd9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:41,053] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:15:41,053] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:15:41,053] [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
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	82.8487	149	1254	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	82.009	70	1254	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	81.4214	281	1254	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	81.2098	325	1254	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	81.1723	328	1254	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	80.9734	269	1254	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	80.9657	169	1254	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	80.9392	329	1254	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	80.7893	270	1254	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	80.7678	314	1254	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	80.3832	257	1254	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.0836	119	1254	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.1927	69	1254	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_900129135.1	341220	341220	suspected-type	True	77.1072	81	1254	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.7579	61	1254	95	below_threshold
Lactonifactor longoviformis	strain=DSM 17459	GCA_002915525.1	341220	341220	suspected-type	True	76.6497	60	1254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:41,055] [INFO] DFAST Taxonomy check result was written to GCF_025566965.1_ASM2556696v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:41,056] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:41,056] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:41,056] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2142dacd-51be-4160-84e9-c3a753abbd9e/dqc_reference/checkm_data
[2024-01-25 20:15:41,057] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:41,096] [INFO] Task started: CheckM
[2024-01-25 20:15:41,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025566965.1_ASM2556696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025566965.1_ASM2556696v1_genomic.fna/checkm_input GCF_025566965.1_ASM2556696v1_genomic.fna/checkm_result
[2024-01-25 20:16:10,480] [INFO] Task succeeded: CheckM
[2024-01-25 20:16:10,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:16:10,508] [INFO] ===== Completeness check finished =====
[2024-01-25 20:16:10,508] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:16:10,511] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025566965.1_ASM2556696v1_genomic.fna/markers.fasta)
[2024-01-25 20:16:10,511] [INFO] Task started: Blastn
[2024-01-25 20:16:10,512] [INFO] Running command: blastn -query GCF_025566965.1_ASM2556696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2142dacd-51be-4160-84e9-c3a753abbd9e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025566965.1_ASM2556696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:11,548] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:11,550] [INFO] Selected 16 target genomes.
[2024-01-25 20:16:11,551] [INFO] Target genome list was writen to GCF_025566965.1_ASM2556696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:16:11,575] [INFO] Task started: fastANI
[2024-01-25 20:16:11,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5779bfb-3464-4fdf-b442-d6929348f974/GCF_025566965.1_ASM2556696v1_genomic.fna.gz --refList GCF_025566965.1_ASM2556696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025566965.1_ASM2556696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:23,263] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:23,274] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:23,275] [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_013304385.1	s__Blautia_A sp900066505	98.0835	984	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.06	97.97	0.82	0.78	4	conclusive
GCA_900316115.1	s__Blautia_A sp900316115	89.49	709	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.53	99.48	0.92	0.90	3	-
GCF_016908695.1	s__Blautia_A faecis	82.5189	397	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.52	97.01	0.80	0.69	30	-
GCF_013300825.1	s__Blautia_A wexlerae_B	82.2413	318	1254	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_013304735.1	s__Blautia_A sp900066205	82.0728	334	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCF_003460605.1	s__Blautia_A sp900066145	81.9043	392	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.04	98.72	0.92	0.85	9	-
GCF_003461245.1	s__Blautia_A sp000436615	81.2112	269	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.75	98.36	0.88	0.81	8	-
GCF_009707925.1	s__Blautia_A luti	81.1893	326	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.33	97.04	0.87	0.84	5	-
GCF_001487165.1	s__Blautia_A massiliensis	81.1719	328	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.95	95.87	0.85	0.71	55	-
GCF_003471165.1	s__Blautia_A sp003471165	80.9385	308	1254	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_013304825.1	s__Blautia_A schinkii	80.4537	304	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.24	98.34	0.93	0.82	9	-
GCA_900763175.1	s__Blautia_A sp900763175	79.8515	298	1254	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_905206915.1	s__Blautia_A sp905206915	79.0316	230	1254	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_900541985.1	s__Blautia_A sp900541985	78.5719	225	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.92	99.92	0.93	0.93	2	-
GCA_000702025.1	s__Blautia_A schinkii_A	78.5499	204	1254	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_900541345.1	s__Blautia_A sp900541345	78.2641	180	1254	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.52	96.26	0.83	0.75	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:23,276] [INFO] GTDB search result was written to GCF_025566965.1_ASM2556696v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:23,276] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:23,280] [INFO] DFAST_QC result json was written to GCF_025566965.1_ASM2556696v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:23,280] [INFO] DFAST_QC completed!
[2024-01-25 20:16:23,280] [INFO] Total running time: 0h1m3s