[2024-01-24 11:03:48,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:03:48,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:03:48,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e9a4a3a-a4d2-41ad-9cb7-07008ec06fad/dqc_reference
[2024-01-24 11:03:49,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:03:49,361] [INFO] Task started: Prodigal
[2024-01-24 11:03:49,361] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe554285-1dc7-4d6d-bff4-ca8c426a60d2/GCF_016696745.1_ASM1669674v1_genomic.fna.gz | prodigal -d GCF_016696745.1_ASM1669674v1_genomic.fna/cds.fna -a GCF_016696745.1_ASM1669674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:04:02,818] [INFO] Task succeeded: Prodigal
[2024-01-24 11:04:02,818] [INFO] Task started: HMMsearch
[2024-01-24 11:04:02,819] [INFO] Running command: hmmsearch --tblout GCF_016696745.1_ASM1669674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e9a4a3a-a4d2-41ad-9cb7-07008ec06fad/dqc_reference/reference_markers.hmm GCF_016696745.1_ASM1669674v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:04:03,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:04:03,159] [INFO] Found 6/6 markers.
[2024-01-24 11:04:03,206] [INFO] Query marker FASTA was written to GCF_016696745.1_ASM1669674v1_genomic.fna/markers.fasta
[2024-01-24 11:04:03,206] [INFO] Task started: Blastn
[2024-01-24 11:04:03,207] [INFO] Running command: blastn -query GCF_016696745.1_ASM1669674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e9a4a3a-a4d2-41ad-9cb7-07008ec06fad/dqc_reference/reference_markers.fasta -out GCF_016696745.1_ASM1669674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:03,841] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:03,845] [INFO] Selected 11 target genomes.
[2024-01-24 11:04:03,845] [INFO] Target genome list was writen to GCF_016696745.1_ASM1669674v1_genomic.fna/target_genomes.txt
[2024-01-24 11:04:03,861] [INFO] Task started: fastANI
[2024-01-24 11:04:03,862] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe554285-1dc7-4d6d-bff4-ca8c426a60d2/GCF_016696745.1_ASM1669674v1_genomic.fna.gz --refList GCF_016696745.1_ASM1669674v1_genomic.fna/target_genomes.txt --output GCF_016696745.1_ASM1669674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:04:14,688] [INFO] Task succeeded: fastANI
[2024-01-24 11:04:14,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e9a4a3a-a4d2-41ad-9cb7-07008ec06fad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:04:14,689] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e9a4a3a-a4d2-41ad-9cb7-07008ec06fad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:04:14,703] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:04:14,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:04:14,704] [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
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	100.0	1708	1709	95	conclusive
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	100.0	1709	1709	95	conclusive
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	99.999	1707	1709	95	conclusive
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	94.2039	1298	1709	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	85.3884	1119	1709	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	85.3794	1157	1709	95	below_threshold
Anaerostipes rhamnosivorans	strain=1y2	GCA_005280655.1	1229621	1229621	type	True	79.1779	59	1709	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.1892	79	1709	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	77.8895	77	1709	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	77.3182	128	1709	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.7128	79	1709	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:04:14,706] [INFO] DFAST Taxonomy check result was written to GCF_016696745.1_ASM1669674v1_genomic.fna/tc_result.tsv
[2024-01-24 11:04:14,706] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:04:14,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:04:14,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e9a4a3a-a4d2-41ad-9cb7-07008ec06fad/dqc_reference/checkm_data
[2024-01-24 11:04:14,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:04:14,755] [INFO] Task started: CheckM
[2024-01-24 11:04:14,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016696745.1_ASM1669674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016696745.1_ASM1669674v1_genomic.fna/checkm_input GCF_016696745.1_ASM1669674v1_genomic.fna/checkm_result
[2024-01-24 11:04:57,593] [INFO] Task succeeded: CheckM
[2024-01-24 11:04:57,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:04:57,617] [INFO] ===== Completeness check finished =====
[2024-01-24 11:04:57,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:04:57,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016696745.1_ASM1669674v1_genomic.fna/markers.fasta)
[2024-01-24 11:04:57,619] [INFO] Task started: Blastn
[2024-01-24 11:04:57,619] [INFO] Running command: blastn -query GCF_016696745.1_ASM1669674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e9a4a3a-a4d2-41ad-9cb7-07008ec06fad/dqc_reference/reference_markers_gtdb.fasta -out GCF_016696745.1_ASM1669674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:58,643] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:58,647] [INFO] Selected 11 target genomes.
[2024-01-24 11:04:58,647] [INFO] Target genome list was writen to GCF_016696745.1_ASM1669674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:04:58,662] [INFO] Task started: fastANI
[2024-01-24 11:04:58,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe554285-1dc7-4d6d-bff4-ca8c426a60d2/GCF_016696745.1_ASM1669674v1_genomic.fna.gz --refList GCF_016696745.1_ASM1669674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016696745.1_ASM1669674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:07,869] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:07,883] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:05:07,883] [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_001689125.2	s__Blautia pseudococcoides	99.999	1707	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.82	99.56	0.97	0.91	7	conclusive
GCA_002270465.1	s__Blautia hominis	94.1835	1241	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.84	98.04	0.89	0.81	4	-
GCF_014287615.1	s__Blautia sp001304935	85.6078	1199	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.32	98.73	0.92	0.87	9	-
GCF_900461125.1	s__Blautia coccoides	85.4181	1165	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.33	97.47	0.84	0.79	11	-
GCA_003481745.1	s__Blautia stercoris	78.1861	200	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.69	97.83	0.91	0.84	8	-
GCF_002161285.1	s__Blautia ornithocaccae	77.7731	222	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	98.34	98.05	0.87	0.83	4	-
GCA_018374355.1	s__Oliverpabstia sp018374355	77.6225	132	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765525.1	s__Blautia pullicola	77.595	181	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.10	98.67	0.84	0.76	4	-
GCF_000403845.2	s__14-2 sp000403845	77.5097	84	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556555.1	s__Blautia sp900556555	77.1969	131	1709	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:05:07,885] [INFO] GTDB search result was written to GCF_016696745.1_ASM1669674v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:07,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:07,889] [INFO] DFAST_QC result json was written to GCF_016696745.1_ASM1669674v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:07,889] [INFO] DFAST_QC completed!
[2024-01-24 11:05:07,889] [INFO] Total running time: 0h1m20s