[2024-01-24 12:22:48,370] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:48,372] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:48,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgebd7cd76-872b-4820-83b8-00fa671035d1/dqc_reference
[2024-01-24 12:22:49,598] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:49,599] [INFO] Task started: Prodigal
[2024-01-24 12:22:49,599] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dfa56f4-7c2d-48d7-b5fe-42e59bc455a9/GCF_001045675.1_ASM104567v1_genomic.fna.gz | prodigal -d GCF_001045675.1_ASM104567v1_genomic.fna/cds.fna -a GCF_001045675.1_ASM104567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:57,708] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:57,708] [INFO] Task started: HMMsearch
[2024-01-24 12:22:57,708] [INFO] Running command: hmmsearch --tblout GCF_001045675.1_ASM104567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebd7cd76-872b-4820-83b8-00fa671035d1/dqc_reference/reference_markers.hmm GCF_001045675.1_ASM104567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:57,906] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:57,907] [INFO] Found 6/6 markers.
[2024-01-24 12:22:57,937] [INFO] Query marker FASTA was written to GCF_001045675.1_ASM104567v1_genomic.fna/markers.fasta
[2024-01-24 12:22:57,937] [INFO] Task started: Blastn
[2024-01-24 12:22:57,937] [INFO] Running command: blastn -query GCF_001045675.1_ASM104567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebd7cd76-872b-4820-83b8-00fa671035d1/dqc_reference/reference_markers.fasta -out GCF_001045675.1_ASM104567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:58,546] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:58,550] [INFO] Selected 17 target genomes.
[2024-01-24 12:22:58,550] [INFO] Target genome list was writen to GCF_001045675.1_ASM104567v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:58,557] [INFO] Task started: fastANI
[2024-01-24 12:22:58,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dfa56f4-7c2d-48d7-b5fe-42e59bc455a9/GCF_001045675.1_ASM104567v1_genomic.fna.gz --refList GCF_001045675.1_ASM104567v1_genomic.fna/target_genomes.txt --output GCF_001045675.1_ASM104567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:06,448] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:06,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebd7cd76-872b-4820-83b8-00fa671035d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:06,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebd7cd76-872b-4820-83b8-00fa671035d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:06,458] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:23:06,458] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:06,458] [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
Megasphaera cerevisiae	strain=DSM 20462	GCA_001045675.1	39029	39029	type	True	100.0	991	995	95	conclusive
Megasphaera cerevisiae	strain=DSM 20462	GCA_900167325.1	39029	39029	type	True	99.9639	967	995	95	conclusive
Megasphaera paucivorans	strain=DSM 16981	GCA_900103535.1	349095	349095	type	True	79.5518	163	995	95	below_threshold
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	77.7399	137	995	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	77.5598	173	995	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	77.367	170	995	95	below_threshold
Megasphaera hutchinsoni	strain=KA00182	GCA_001553405.1	1588748	1588748	type	True	77.2145	56	995	95	below_threshold
Megasphaera lornae	strain=UPII 199-6	GCA_000214495.2	1000568	1000568	type	True	77.1432	83	995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:06,460] [INFO] DFAST Taxonomy check result was written to GCF_001045675.1_ASM104567v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:06,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:06,462] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:06,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebd7cd76-872b-4820-83b8-00fa671035d1/dqc_reference/checkm_data
[2024-01-24 12:23:06,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:06,497] [INFO] Task started: CheckM
[2024-01-24 12:23:06,498] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001045675.1_ASM104567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001045675.1_ASM104567v1_genomic.fna/checkm_input GCF_001045675.1_ASM104567v1_genomic.fna/checkm_result
[2024-01-24 12:23:34,790] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:34,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:34,850] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:34,850] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:34,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001045675.1_ASM104567v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:34,851] [INFO] Task started: Blastn
[2024-01-24 12:23:34,851] [INFO] Running command: blastn -query GCF_001045675.1_ASM104567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebd7cd76-872b-4820-83b8-00fa671035d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_001045675.1_ASM104567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:35,728] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:35,733] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:35,733] [INFO] Target genome list was writen to GCF_001045675.1_ASM104567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:35,829] [INFO] Task started: fastANI
[2024-01-24 12:23:35,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dfa56f4-7c2d-48d7-b5fe-42e59bc455a9/GCF_001045675.1_ASM104567v1_genomic.fna.gz --refList GCF_001045675.1_ASM104567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001045675.1_ASM104567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:45,369] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:45,384] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:45,384] [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_001045675.1	s__Megasphaera cerevisiae	100.0	991	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.73	99.50	0.95	0.92	3	conclusive
GCF_900103535.1	s__Megasphaera_A paucivorans	79.5022	160	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000417505.1	s__Megasphaera sp000417505	78.2155	133	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCA_002431345.1	s__Megasphaera sp002431345	77.7882	216	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.44	99.22	0.90	0.87	5	-
GCF_003010495.1	s__Megasphaera elsdenii	77.7651	136	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	-
GCA_902388315.1	s__Megasphaera sp902388315	77.6765	108	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCF_003367905.1	s__Megasphaera stantonii	77.5769	172	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	97.46	96.44	0.91	0.87	8	-
GCA_900095875.1	s__Caecibacter massiliensis	77.5167	120	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.76	97.64	0.92	0.86	18	-
GCA_900554215.1	s__Megasphaera sp900554215	77.493	122	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	95.76	95.76	0.83	0.83	2	-
GCA_002319965.1	s__Megasphaera sp002319965	77.4225	119	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
GCF_001553405.1	s__Megasphaera hutchinsoni	77.1709	57	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.62	98.30	0.94	0.92	5	-
GCF_000214495.1	s__Megasphaera lornae	77.1432	83	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.01	98.81	0.95	0.94	5	-
GCA_900539295.1	s__Megasphaera sp900539295	77.1366	120	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900752195.1	s__Caecibacter sp900549385	76.8642	103	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	99.73	99.52	0.95	0.92	4	-
GCF_000239275.1	s__Anaeroglobus geminatus	76.6557	66	995	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	98.83	98.46	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:45,385] [INFO] GTDB search result was written to GCF_001045675.1_ASM104567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:45,386] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:45,391] [INFO] DFAST_QC result json was written to GCF_001045675.1_ASM104567v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:45,392] [INFO] DFAST_QC completed!
[2024-01-24 12:23:45,392] [INFO] Total running time: 0h0m57s