[2024-01-25 19:55:50,573] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:50,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:50,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fdb7757-efae-4a98-aba0-c56ab63d7752/dqc_reference
[2024-01-25 19:55:51,744] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:51,745] [INFO] Task started: Prodigal
[2024-01-25 19:55:51,745] [INFO] Running command: gunzip -c /var/lib/cwl/stg570f54b5-45a8-4c1f-b526-d78aa6f6ba0e/GCF_000299355.1_ASM29935v1_genomic.fna.gz | prodigal -d GCF_000299355.1_ASM29935v1_genomic.fna/cds.fna -a GCF_000299355.1_ASM29935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:55,981] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:55,981] [INFO] Task started: HMMsearch
[2024-01-25 19:55:55,981] [INFO] Running command: hmmsearch --tblout GCF_000299355.1_ASM29935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fdb7757-efae-4a98-aba0-c56ab63d7752/dqc_reference/reference_markers.hmm GCF_000299355.1_ASM29935v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:56,178] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:56,179] [INFO] Found 6/6 markers.
[2024-01-25 19:55:56,206] [INFO] Query marker FASTA was written to GCF_000299355.1_ASM29935v1_genomic.fna/markers.fasta
[2024-01-25 19:55:56,207] [INFO] Task started: Blastn
[2024-01-25 19:55:56,207] [INFO] Running command: blastn -query GCF_000299355.1_ASM29935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fdb7757-efae-4a98-aba0-c56ab63d7752/dqc_reference/reference_markers.fasta -out GCF_000299355.1_ASM29935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:56,737] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:56,740] [INFO] Selected 18 target genomes.
[2024-01-25 19:55:56,740] [INFO] Target genome list was writen to GCF_000299355.1_ASM29935v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:56,754] [INFO] Task started: fastANI
[2024-01-25 19:55:56,755] [INFO] Running command: fastANI --query /var/lib/cwl/stg570f54b5-45a8-4c1f-b526-d78aa6f6ba0e/GCF_000299355.1_ASM29935v1_genomic.fna.gz --refList GCF_000299355.1_ASM29935v1_genomic.fna/target_genomes.txt --output GCF_000299355.1_ASM29935v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:06,729] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:06,729] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fdb7757-efae-4a98-aba0-c56ab63d7752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:06,730] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fdb7757-efae-4a98-aba0-c56ab63d7752/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:06,740] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:56:06,740] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:06,740] [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
Gottschalkia acidurici	strain=9a	GCA_000299355.1	1556	1556	type	True	100.0	1035	1035	95	conclusive
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	77.3381	90	1035	95	below_threshold
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	76.6402	94	1035	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	76.5585	82	1035	95	below_threshold
Senegalia massiliensis	strain=SIT17	GCA_900626135.1	1720316	1720316	type	True	76.3288	109	1035	95	below_threshold
Proteiniborus ethanoligenes	strain=DSM 21650	GCA_900107485.1	415015	415015	type	True	75.9063	91	1035	95	below_threshold
Caloranaerobacter ferrireducens	strain=DY22619	GCA_001730685.1	1323370	1323370	type	True	75.7689	59	1035	95	below_threshold
Abyssisolibacter fermentans	strain=MCWD3	GCA_001559865.1	1766203	1766203	type	True	75.7632	86	1035	95	below_threshold
Clostridiisalibacter paucivorans	strain=DSM 22131	GCA_000620125.1	408753	408753	type	True	75.7453	75	1035	95	below_threshold
Tepidibacter thalassicus	strain=DSM 15285	GCA_900129915.1	214905	214905	type	True	75.7447	68	1035	95	below_threshold
Anaeromonas frigoriresistens	strain=D2Q-11	GCA_016820655.1	2683708	2683708	type	True	75.6657	81	1035	95	below_threshold
Caloranaerobacter azorensis	strain=DSM 13643	GCA_900129995.1	116090	116090	type	True	75.6159	59	1035	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	75.6094	88	1035	95	below_threshold
Sporosalibacterium faouarense	strain=SOL3f37	GCA_016765695.1	516123	516123	type	True	75.442	87	1035	95	below_threshold
Anaeromicrobium sediminis	strain=DY2726D	GCA_002270055.1	1478221	1478221	type	True	75.2542	76	1035	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	75.0975	74	1035	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:06,742] [INFO] DFAST Taxonomy check result was written to GCF_000299355.1_ASM29935v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:06,742] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:06,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:06,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fdb7757-efae-4a98-aba0-c56ab63d7752/dqc_reference/checkm_data
[2024-01-25 19:56:06,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:06,777] [INFO] Task started: CheckM
[2024-01-25 19:56:06,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000299355.1_ASM29935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000299355.1_ASM29935v1_genomic.fna/checkm_input GCF_000299355.1_ASM29935v1_genomic.fna/checkm_result
[2024-01-25 19:56:25,945] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:25,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:25,962] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:25,963] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:25,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000299355.1_ASM29935v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:25,963] [INFO] Task started: Blastn
[2024-01-25 19:56:25,963] [INFO] Running command: blastn -query GCF_000299355.1_ASM29935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0fdb7757-efae-4a98-aba0-c56ab63d7752/dqc_reference/reference_markers_gtdb.fasta -out GCF_000299355.1_ASM29935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:26,710] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:26,713] [INFO] Selected 24 target genomes.
[2024-01-25 19:56:26,713] [INFO] Target genome list was writen to GCF_000299355.1_ASM29935v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:26,751] [INFO] Task started: fastANI
[2024-01-25 19:56:26,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg570f54b5-45a8-4c1f-b526-d78aa6f6ba0e/GCF_000299355.1_ASM29935v1_genomic.fna.gz --refList GCF_000299355.1_ASM29935v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000299355.1_ASM29935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:39,338] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:39,349] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:39,349] [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_000299355.1	s__Gottschalkia acidurici	100.0	1035	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Gottschalkiaceae;g__Gottschalkia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001584565.1	s__Clostridium_Y paradoxum	77.798	64	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridium_Y	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900095305.1	s__Proteiniborus sp900095305	76.6103	101	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695605.1	s__DSM105185 sp009695605	76.6034	93	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__DSM105185	95.0	99.10	99.10	0.90	0.90	2	-
GCA_002029295.1	s__Clostridium_Y thermoalcaliphilum	76.4365	54	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridium_Y	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911265.1	s__Senegalia massiliensis_A	76.3321	103	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376545.1	s__Proteiniborus sp002376545	76.2951	78	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	99.93	99.93	0.97	0.97	2	-
GCF_900626135.1	s__Senegalia massiliensis	76.238	109	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001006285.1	s__Paraclostridium benzoelyticum	75.9854	79	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Paraclostridium	95.4733	N/A	N/A	N/A	N/A	1	-
GCF_900107485.1	s__Proteiniborus ethanoligenes	75.9063	91	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Proteiniboraceae;g__Proteiniborus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730685.1	s__Caloranaerobacter ferrireducens	75.7689	59	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Thermohalobacteraceae;g__Caloranaerobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620125.1	s__Clostridiisalibacter paucivorans	75.7453	75	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Clostridiisalibacteraceae;g__Clostridiisalibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129915.1	s__Tepidibacter thalassicus	75.7447	68	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Tepidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820655.1	s__Senegalia sp016820655	75.6657	81	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__SIT17;g__Senegalia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002270055.1	s__Anaeromicrobium sediminis	75.2542	76	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Thermotaleaceae;g__Anaeromicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:39,350] [INFO] GTDB search result was written to GCF_000299355.1_ASM29935v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:39,351] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:39,355] [INFO] DFAST_QC result json was written to GCF_000299355.1_ASM29935v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:39,355] [INFO] DFAST_QC completed!
[2024-01-25 19:56:39,355] [INFO] Total running time: 0h0m49s