[2024-01-24 12:37:09,732] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:09,734] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:09,734] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ad02355-a1df-4b2c-8077-4ee8ea336617/dqc_reference
[2024-01-24 12:37:11,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:11,082] [INFO] Task started: Prodigal
[2024-01-24 12:37:11,082] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfb3dae4-5e14-4aba-9178-632c479476c4/GCF_004345005.1_ASM434500v1_genomic.fna.gz | prodigal -d GCF_004345005.1_ASM434500v1_genomic.fna/cds.fna -a GCF_004345005.1_ASM434500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:20,552] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:20,552] [INFO] Task started: HMMsearch
[2024-01-24 12:37:20,553] [INFO] Running command: hmmsearch --tblout GCF_004345005.1_ASM434500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ad02355-a1df-4b2c-8077-4ee8ea336617/dqc_reference/reference_markers.hmm GCF_004345005.1_ASM434500v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:20,821] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:20,822] [INFO] Found 6/6 markers.
[2024-01-24 12:37:20,857] [INFO] Query marker FASTA was written to GCF_004345005.1_ASM434500v1_genomic.fna/markers.fasta
[2024-01-24 12:37:20,857] [INFO] Task started: Blastn
[2024-01-24 12:37:20,857] [INFO] Running command: blastn -query GCF_004345005.1_ASM434500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad02355-a1df-4b2c-8077-4ee8ea336617/dqc_reference/reference_markers.fasta -out GCF_004345005.1_ASM434500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:21,545] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:21,550] [INFO] Selected 18 target genomes.
[2024-01-24 12:37:21,551] [INFO] Target genome list was writen to GCF_004345005.1_ASM434500v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:21,567] [INFO] Task started: fastANI
[2024-01-24 12:37:21,567] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb3dae4-5e14-4aba-9178-632c479476c4/GCF_004345005.1_ASM434500v1_genomic.fna.gz --refList GCF_004345005.1_ASM434500v1_genomic.fna/target_genomes.txt --output GCF_004345005.1_ASM434500v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:31,764] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:31,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ad02355-a1df-4b2c-8077-4ee8ea336617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:31,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ad02355-a1df-4b2c-8077-4ee8ea336617/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:31,781] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:31,782] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:31,782] [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
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	82.7036	725	1199	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	82.6692	734	1199	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	79.2054	289	1199	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	79.1537	297	1199	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	78.9973	173	1199	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.0003	94	1199	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	77.9348	60	1199	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.8092	92	1199	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.7146	140	1199	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.4837	84	1199	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.3548	101	1199	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	77.0708	80	1199	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:31,783] [INFO] DFAST Taxonomy check result was written to GCF_004345005.1_ASM434500v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:31,784] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:31,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:31,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ad02355-a1df-4b2c-8077-4ee8ea336617/dqc_reference/checkm_data
[2024-01-24 12:37:31,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:31,823] [INFO] Task started: CheckM
[2024-01-24 12:37:31,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004345005.1_ASM434500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004345005.1_ASM434500v1_genomic.fna/checkm_input GCF_004345005.1_ASM434500v1_genomic.fna/checkm_result
[2024-01-24 12:38:04,161] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:04,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:04,184] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:04,184] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:04,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004345005.1_ASM434500v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:04,185] [INFO] Task started: Blastn
[2024-01-24 12:38:04,185] [INFO] Running command: blastn -query GCF_004345005.1_ASM434500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad02355-a1df-4b2c-8077-4ee8ea336617/dqc_reference/reference_markers_gtdb.fasta -out GCF_004345005.1_ASM434500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:05,255] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:05,258] [INFO] Selected 8 target genomes.
[2024-01-24 12:38:05,258] [INFO] Target genome list was writen to GCF_004345005.1_ASM434500v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:05,291] [INFO] Task started: fastANI
[2024-01-24 12:38:05,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfb3dae4-5e14-4aba-9178-632c479476c4/GCF_004345005.1_ASM434500v1_genomic.fna.gz --refList GCF_004345005.1_ASM434500v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004345005.1_ASM434500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:11,883] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:11,890] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:11,890] [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_004345005.1	s__Extibacter muris	100.0	1198	1199	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	95.70	95.67	0.77	0.77	4	conclusive
GCF_017566055.1	s__Extibacter sp017566055	93.0922	897	1199	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001185345.1	s__Extibacter sp001185345	90.0483	889	1199	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008281175.1	s__Extibacter hylemonae	82.7036	725	1199	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	99.20	98.44	0.97	0.93	5	-
GCF_004295125.1	s__Clostridium_AP scindens	79.1537	297	1199	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.44	99.12	0.90	0.78	13	-
GCA_900553355.1	s__Merdimonas sp900553355	77.1527	136	1199	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003489085.1	s__UBA9414 sp003489085	75.7384	52	1199	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:11,892] [INFO] GTDB search result was written to GCF_004345005.1_ASM434500v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:11,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:11,896] [INFO] DFAST_QC result json was written to GCF_004345005.1_ASM434500v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:11,896] [INFO] DFAST_QC completed!
[2024-01-24 12:38:11,896] [INFO] Total running time: 0h1m2s