[2024-01-24 14:15:02,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,557] [INFO] DQC Reference Directory: /var/lib/cwl/stg72020a37-3d03-46ef-b634-351bebfc297e/dqc_reference
[2024-01-24 14:15:04,175] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:04,176] [INFO] Task started: Prodigal
[2024-01-24 14:15:04,176] [INFO] Running command: gunzip -c /var/lib/cwl/stg09adc19e-f3b4-4d9c-9a2c-a1cfc39f30fe/GCF_006861675.1_ASM686167v1_genomic.fna.gz | prodigal -d GCF_006861675.1_ASM686167v1_genomic.fna/cds.fna -a GCF_006861675.1_ASM686167v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:08,270] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:08,271] [INFO] Task started: HMMsearch
[2024-01-24 14:15:08,271] [INFO] Running command: hmmsearch --tblout GCF_006861675.1_ASM686167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72020a37-3d03-46ef-b634-351bebfc297e/dqc_reference/reference_markers.hmm GCF_006861675.1_ASM686167v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:08,512] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:08,513] [INFO] Found 6/6 markers.
[2024-01-24 14:15:08,538] [INFO] Query marker FASTA was written to GCF_006861675.1_ASM686167v1_genomic.fna/markers.fasta
[2024-01-24 14:15:08,539] [INFO] Task started: Blastn
[2024-01-24 14:15:08,539] [INFO] Running command: blastn -query GCF_006861675.1_ASM686167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72020a37-3d03-46ef-b634-351bebfc297e/dqc_reference/reference_markers.fasta -out GCF_006861675.1_ASM686167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:09,249] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:09,254] [INFO] Selected 18 target genomes.
[2024-01-24 14:15:09,255] [INFO] Target genome list was writen to GCF_006861675.1_ASM686167v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:09,271] [INFO] Task started: fastANI
[2024-01-24 14:15:09,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg09adc19e-f3b4-4d9c-9a2c-a1cfc39f30fe/GCF_006861675.1_ASM686167v1_genomic.fna.gz --refList GCF_006861675.1_ASM686167v1_genomic.fna/target_genomes.txt --output GCF_006861675.1_ASM686167v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:18,164] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:18,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72020a37-3d03-46ef-b634-351bebfc297e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:18,165] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72020a37-3d03-46ef-b634-351bebfc297e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:18,177] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:18,177] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:18,178] [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
Peptacetobacter hominis	strain=ZHW00191	GCA_006861675.1	2743610	2743610	type	True	100.0	695	696	95	conclusive
Peptacetobacter hiranonis	strain=DSM 13275	GCA_008151785.1	89152	89152	type	True	80.2326	318	696	95	below_threshold
Peptacetobacter hiranonis	strain=DSM 13275	GCA_000156055.1	89152	89152	type	True	80.1355	322	696	95	below_threshold
Terrisporobacter othiniensis	strain=08-306576	GCA_000808015.1	1577792	1577792	type	True	77.37	108	696	95	below_threshold
Romboutsia ilealis	strain=CRIB	GCA_900015215.1	1115758	1115758	type	True	77.3543	100	696	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	77.3537	120	696	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	77.3153	93	696	95	below_threshold
Intestinibacter bartlettii	strain=DSM 16795	GCA_000154445.1	261299	261299	type	True	77.1899	102	696	95	below_threshold
Romboutsia lituseburensis	strain=A25K	GCA_900002825.1	1537	1537	type	True	77.1716	113	696	95	below_threshold
Intestinibacter bartlettii	strain=DSM 16795	GCA_900167285.1	261299	261299	type	True	77.1081	105	696	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_006802875.1	1490	1490	type	True	77.0527	105	696	95	below_threshold
Romboutsia lituseburensis	strain=DSM 797	GCA_900103615.1	1537	1537	type	True	77.0301	110	696	95	below_threshold
[Clostridium] dakarense	strain=FF1	GCA_000499525.1	1301100	1301100	type	True	76.9725	120	696	95	below_threshold
Clostridioides mangenotii	strain=DSM 1289	GCA_017873185.1	1540	1540	suspected-type	True	76.9542	100	696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:18,180] [INFO] DFAST Taxonomy check result was written to GCF_006861675.1_ASM686167v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:18,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:18,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:18,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72020a37-3d03-46ef-b634-351bebfc297e/dqc_reference/checkm_data
[2024-01-24 14:15:18,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:18,209] [INFO] Task started: CheckM
[2024-01-24 14:15:18,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006861675.1_ASM686167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006861675.1_ASM686167v1_genomic.fna/checkm_input GCF_006861675.1_ASM686167v1_genomic.fna/checkm_result
[2024-01-24 14:15:37,989] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:37,990] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:38,008] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:38,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:38,009] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006861675.1_ASM686167v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:38,009] [INFO] Task started: Blastn
[2024-01-24 14:15:38,010] [INFO] Running command: blastn -query GCF_006861675.1_ASM686167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72020a37-3d03-46ef-b634-351bebfc297e/dqc_reference/reference_markers_gtdb.fasta -out GCF_006861675.1_ASM686167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:38,818] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:38,821] [INFO] Selected 14 target genomes.
[2024-01-24 14:15:38,821] [INFO] Target genome list was writen to GCF_006861675.1_ASM686167v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:38,850] [INFO] Task started: fastANI
[2024-01-24 14:15:38,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg09adc19e-f3b4-4d9c-9a2c-a1cfc39f30fe/GCF_006861675.1_ASM686167v1_genomic.fna.gz --refList GCF_006861675.1_ASM686167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006861675.1_ASM686167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:45,082] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:45,092] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:45,093] [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_006861675.1	s__Peptacetobacter hominis	100.0	695	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900539645.1	s__Peptacetobacter sp900539645	80.367	272	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	97.26	95.86	0.91	0.87	4	-
GCF_008151785.1	s__Peptacetobacter hiranonis	80.2451	316	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	97.84	95.69	0.88	0.73	5	-
GCA_900550335.1	s__Peptacetobacter sp900550335	79.9366	239	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Peptacetobacter	95.0	99.93	99.93	0.85	0.85	2	-
GCF_900015215.1	s__Romboutsia ilealis	77.3503	101	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.59	98.59	0.90	0.90	2	-
GCF_900106845.1	s__Romboutsia timonensis	77.3219	123	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	98.20	98.12	0.88	0.86	5	-
GCA_018336475.1	s__Romboutsia sp018336475	77.2601	109	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Romboutsia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012317385.1	s__GCA-900066495 sp900545985	77.2522	105	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	98.78	98.75	0.89	0.89	3	-
GCF_006802875.1	s__Paraclostridium bifermentans	77.0514	105	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	96.2286	97.64	96.79	0.90	0.86	14	-
GCA_900604495.1	s__GCA-900066495 sp900066495	77.022	105	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	99.74	99.60	0.96	0.94	5	-
GCA_017425305.1	s__Paraclostridium sp017425305	76.5527	54	696	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.0	97.54	97.54	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:45,098] [INFO] GTDB search result was written to GCF_006861675.1_ASM686167v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:45,099] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:45,103] [INFO] DFAST_QC result json was written to GCF_006861675.1_ASM686167v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:45,103] [INFO] DFAST_QC completed!
[2024-01-24 14:15:45,104] [INFO] Total running time: 0h0m43s