[2023-06-05 03:38:41,981] [INFO] DFAST_QC pipeline started.
[2023-06-05 03:38:41,983] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 03:38:41,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d863c13-47c3-406c-b38f-da08629be983/dqc_reference
[2023-06-05 03:38:43,287] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 03:38:43,288] [INFO] Task started: Prodigal
[2023-06-05 03:38:43,288] [INFO] Running command: gunzip -c /var/lib/cwl/stge33dc4ec-256c-48cb-b4b4-158c4be24596/GCA_934754805.1_ERR7738171_bin.64_genomic.fna.gz | prodigal -d GCA_934754805.1_ERR7738171_bin.64_genomic.fna/cds.fna -a GCA_934754805.1_ERR7738171_bin.64_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 03:38:47,142] [INFO] Task succeeded: Prodigal
[2023-06-05 03:38:47,143] [INFO] Task started: HMMsearch
[2023-06-05 03:38:47,143] [INFO] Running command: hmmsearch --tblout GCA_934754805.1_ERR7738171_bin.64_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d863c13-47c3-406c-b38f-da08629be983/dqc_reference/reference_markers.hmm GCA_934754805.1_ERR7738171_bin.64_genomic.fna/protein.faa > /dev/null
[2023-06-05 03:38:47,407] [INFO] Task succeeded: HMMsearch
[2023-06-05 03:38:47,409] [INFO] Found 6/6 markers.
[2023-06-05 03:38:47,435] [INFO] Query marker FASTA was written to GCA_934754805.1_ERR7738171_bin.64_genomic.fna/markers.fasta
[2023-06-05 03:38:47,435] [INFO] Task started: Blastn
[2023-06-05 03:38:47,436] [INFO] Running command: blastn -query GCA_934754805.1_ERR7738171_bin.64_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d863c13-47c3-406c-b38f-da08629be983/dqc_reference/reference_markers.fasta -out GCA_934754805.1_ERR7738171_bin.64_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:38:48,128] [INFO] Task succeeded: Blastn
[2023-06-05 03:38:48,132] [INFO] Selected 21 target genomes.
[2023-06-05 03:38:48,133] [INFO] Target genome list was writen to GCA_934754805.1_ERR7738171_bin.64_genomic.fna/target_genomes.txt
[2023-06-05 03:38:48,135] [INFO] Task started: fastANI
[2023-06-05 03:38:48,135] [INFO] Running command: fastANI --query /var/lib/cwl/stge33dc4ec-256c-48cb-b4b4-158c4be24596/GCA_934754805.1_ERR7738171_bin.64_genomic.fna.gz --refList GCA_934754805.1_ERR7738171_bin.64_genomic.fna/target_genomes.txt --output GCA_934754805.1_ERR7738171_bin.64_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 03:39:01,637] [INFO] Task succeeded: fastANI
[2023-06-05 03:39:01,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d863c13-47c3-406c-b38f-da08629be983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 03:39:01,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d863c13-47c3-406c-b38f-da08629be983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 03:39:01,653] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 03:39:01,653] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 03:39:01,653] [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 saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	85.3585	676	875	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	81.9391	529	875	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	78.4286	311	875	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.4148	313	875	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	78.3349	322	875	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	78.2184	312	875	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	78.1351	338	875	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.9209	242	875	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	77.6409	249	875	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	77.6239	229	875	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.5752	240	875	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.5713	235	875	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	77.567	256	875	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.5173	208	875	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.0081	193	875	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.8258	226	875	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	75.7689	124	875	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 03:39:01,657] [INFO] DFAST Taxonomy check result was written to GCA_934754805.1_ERR7738171_bin.64_genomic.fna/tc_result.tsv
[2023-06-05 03:39:01,658] [INFO] ===== Taxonomy check completed =====
[2023-06-05 03:39:01,658] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 03:39:01,659] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d863c13-47c3-406c-b38f-da08629be983/dqc_reference/checkm_data
[2023-06-05 03:39:01,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 03:39:01,693] [INFO] Task started: CheckM
[2023-06-05 03:39:01,694] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934754805.1_ERR7738171_bin.64_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934754805.1_ERR7738171_bin.64_genomic.fna/checkm_input GCA_934754805.1_ERR7738171_bin.64_genomic.fna/checkm_result
[2023-06-05 03:39:21,336] [INFO] Task succeeded: CheckM
[2023-06-05 03:39:21,337] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 03:39:21,359] [INFO] ===== Completeness check finished =====
[2023-06-05 03:39:21,359] [INFO] ===== Start GTDB Search =====
[2023-06-05 03:39:21,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934754805.1_ERR7738171_bin.64_genomic.fna/markers.fasta)
[2023-06-05 03:39:21,360] [INFO] Task started: Blastn
[2023-06-05 03:39:21,360] [INFO] Running command: blastn -query GCA_934754805.1_ERR7738171_bin.64_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d863c13-47c3-406c-b38f-da08629be983/dqc_reference/reference_markers_gtdb.fasta -out GCA_934754805.1_ERR7738171_bin.64_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 03:39:22,210] [INFO] Task succeeded: Blastn
[2023-06-05 03:39:22,215] [INFO] Selected 14 target genomes.
[2023-06-05 03:39:22,215] [INFO] Target genome list was writen to GCA_934754805.1_ERR7738171_bin.64_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 03:39:22,221] [INFO] Task started: fastANI
[2023-06-05 03:39:22,222] [INFO] Running command: fastANI --query /var/lib/cwl/stge33dc4ec-256c-48cb-b4b4-158c4be24596/GCA_934754805.1_ERR7738171_bin.64_genomic.fna.gz --refList GCA_934754805.1_ERR7738171_bin.64_genomic.fna/target_genomes_gtdb.txt --output GCA_934754805.1_ERR7738171_bin.64_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 03:39:32,212] [INFO] Task succeeded: fastANI
[2023-06-05 03:39:32,229] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 03:39:32,230] [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_900540255.1	s__Clostridium sp900540255	98.7446	755	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	conclusive
GCF_000577815.1	s__Clostridium saudiense	85.348	677	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.39	99.24	0.89	0.87	14	-
GCF_015670405.1	s__Clostridium sp015670405	84.9526	673	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547475.1	s__Clostridium sp900547475	83.5916	578	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCF_004353185.1	s__Clostridium cuniculi	83.5723	656	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCA_900543325.1	s__Clostridium sp900543325	83.5614	599	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015555905.1	s__Clostridium sp015555905	83.5057	651	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.95	98.95	0.73	0.73	2	-
GCA_900766315.1	s__Clostridium sp900766315	83.2069	620	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588715.1	s__Clostridium sp910588715	82.9323	575	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015667795.1	s__Clostridium sp015667795	82.8675	628	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000320405.1	s__Clostridium celatum	81.9166	530	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
GCF_002327185.1	s__Clostridium chauvoei	78.4345	312	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCA_900759995.1	s__Clostridium sp900759995	78.0396	283	875	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
--------------------------------------------------------------------------------
[2023-06-05 03:39:32,232] [INFO] GTDB search result was written to GCA_934754805.1_ERR7738171_bin.64_genomic.fna/result_gtdb.tsv
[2023-06-05 03:39:32,232] [INFO] ===== GTDB Search completed =====
[2023-06-05 03:39:32,236] [INFO] DFAST_QC result json was written to GCA_934754805.1_ERR7738171_bin.64_genomic.fna/dqc_result.json
[2023-06-05 03:39:32,236] [INFO] DFAST_QC completed!
[2023-06-05 03:39:32,236] [INFO] Total running time: 0h0m50s