[2024-01-24 13:27:58,883] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3a935ee-c041-4547-a9f7-a7347c5fbe71/dqc_reference
[2024-01-24 13:28:00,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:00,069] [INFO] Task started: Prodigal
[2024-01-24 13:28:00,069] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9806dbb-0b45-46fd-ab2c-d234abc55f96/GCF_000020605.1_ASM2060v1_genomic.fna.gz | prodigal -d GCF_000020605.1_ASM2060v1_genomic.fna/cds.fna -a GCF_000020605.1_ASM2060v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:08,603] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:08,603] [INFO] Task started: HMMsearch
[2024-01-24 13:28:08,603] [INFO] Running command: hmmsearch --tblout GCF_000020605.1_ASM2060v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3a935ee-c041-4547-a9f7-a7347c5fbe71/dqc_reference/reference_markers.hmm GCF_000020605.1_ASM2060v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:08,889] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:08,890] [INFO] Found 6/6 markers.
[2024-01-24 13:28:08,918] [INFO] Query marker FASTA was written to GCF_000020605.1_ASM2060v1_genomic.fna/markers.fasta
[2024-01-24 13:28:08,919] [INFO] Task started: Blastn
[2024-01-24 13:28:08,919] [INFO] Running command: blastn -query GCF_000020605.1_ASM2060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3a935ee-c041-4547-a9f7-a7347c5fbe71/dqc_reference/reference_markers.fasta -out GCF_000020605.1_ASM2060v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:09,558] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:09,561] [INFO] Selected 30 target genomes.
[2024-01-24 13:28:09,561] [INFO] Target genome list was writen to GCF_000020605.1_ASM2060v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:09,597] [INFO] Task started: fastANI
[2024-01-24 13:28:09,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9806dbb-0b45-46fd-ab2c-d234abc55f96/GCF_000020605.1_ASM2060v1_genomic.fna.gz --refList GCF_000020605.1_ASM2060v1_genomic.fna/target_genomes.txt --output GCF_000020605.1_ASM2060v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:24,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:24,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3a935ee-c041-4547-a9f7-a7347c5fbe71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:24,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3a935ee-c041-4547-a9f7-a7347c5fbe71/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:24,714] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:24,715] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:24,715] [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
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	83.4637	80	1149	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	83.0334	113	1149	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	81.5318	93	1149	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	81.3663	162	1149	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	80.9672	170	1149	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	80.8831	97	1149	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	80.8822	133	1149	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	80.6756	69	1149	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	80.417	207	1149	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	80.3473	155	1149	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	80.1289	69	1149	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.5328	154	1149	95	below_threshold
Agathobacter ruminis	strain=JK623	GCA_002735305.1	1712665	1712665	type	True	78.0148	88	1149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:24,717] [INFO] DFAST Taxonomy check result was written to GCF_000020605.1_ASM2060v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:24,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:24,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:24,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3a935ee-c041-4547-a9f7-a7347c5fbe71/dqc_reference/checkm_data
[2024-01-24 13:28:24,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:24,757] [INFO] Task started: CheckM
[2024-01-24 13:28:24,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020605.1_ASM2060v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020605.1_ASM2060v1_genomic.fna/checkm_input GCF_000020605.1_ASM2060v1_genomic.fna/checkm_result
[2024-01-24 13:28:57,911] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:57,912] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:57,931] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:57,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:57,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020605.1_ASM2060v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:57,933] [INFO] Task started: Blastn
[2024-01-24 13:28:57,933] [INFO] Running command: blastn -query GCF_000020605.1_ASM2060v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3a935ee-c041-4547-a9f7-a7347c5fbe71/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020605.1_ASM2060v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:59,018] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:59,022] [INFO] Selected 14 target genomes.
[2024-01-24 13:28:59,022] [INFO] Target genome list was writen to GCF_000020605.1_ASM2060v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:59,039] [INFO] Task started: fastANI
[2024-01-24 13:28:59,039] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9806dbb-0b45-46fd-ab2c-d234abc55f96/GCF_000020605.1_ASM2060v1_genomic.fna.gz --refList GCF_000020605.1_ASM2060v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020605.1_ASM2060v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:07,233] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:07,247] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:07,248] [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
GCA_000020605.1	s__Agathobacter rectalis	100.0	1144	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.37	96.06	0.82	0.65	151	conclusive
GCA_900546625.1	s__Agathobacter sp900546625	94.5155	743	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	96.96	96.96	0.86	0.86	2	-
GCA_900317585.1	s__Agathobacter sp900317585	94.3696	645	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.18	95.52	0.87	0.83	5	-
GCA_905209075.1	s__Agathobacter sp905209075	81.7892	336	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.22	97.67	0.80	0.73	5	-
GCA_900549895.1	s__Agathobacter sp900549895	78.9232	97	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552085.1	s__Agathobacter sp900552085	78.7794	128	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_900548765.1	s__Agathobacter sp900548765	78.5498	176	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	97.03	0.78	0.78	2	-
GCA_017937095.1	s__Roseburia sp017937095	78.1562	96	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543445.1	s__Agathobacter sp900543445	78.1516	143	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
GCA_003483745.1	s__Roseburia sp003483745	77.6892	102	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_002299665.1	s__CAG-45 sp002299665	77.5497	50	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587655.1	s__Agathobacter sp910587655	76.9664	80	1149	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:07,249] [INFO] GTDB search result was written to GCF_000020605.1_ASM2060v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:07,250] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:07,253] [INFO] DFAST_QC result json was written to GCF_000020605.1_ASM2060v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:07,253] [INFO] DFAST_QC completed!
[2024-01-24 13:29:07,253] [INFO] Total running time: 0h1m8s