[2024-01-24 13:49:28,667] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:28,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:28,669] [INFO] DQC Reference Directory: /var/lib/cwl/stged0410c6-7a37-4496-a290-133859bbaab6/dqc_reference
[2024-01-24 13:49:29,864] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:29,865] [INFO] Task started: Prodigal
[2024-01-24 13:49:29,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bacab5a-1dce-4d8b-a790-be70d611c404/GCF_000430995.1_TC1_genomic.fna.gz | prodigal -d GCF_000430995.1_TC1_genomic.fna/cds.fna -a GCF_000430995.1_TC1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:34,185] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:34,185] [INFO] Task started: HMMsearch
[2024-01-24 13:49:34,185] [INFO] Running command: hmmsearch --tblout GCF_000430995.1_TC1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged0410c6-7a37-4496-a290-133859bbaab6/dqc_reference/reference_markers.hmm GCF_000430995.1_TC1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:34,461] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:34,462] [INFO] Found 6/6 markers.
[2024-01-24 13:49:34,498] [INFO] Query marker FASTA was written to GCF_000430995.1_TC1_genomic.fna/markers.fasta
[2024-01-24 13:49:34,498] [INFO] Task started: Blastn
[2024-01-24 13:49:34,498] [INFO] Running command: blastn -query GCF_000430995.1_TC1_genomic.fna/markers.fasta -db /var/lib/cwl/stged0410c6-7a37-4496-a290-133859bbaab6/dqc_reference/reference_markers.fasta -out GCF_000430995.1_TC1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:35,143] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:35,146] [INFO] Selected 24 target genomes.
[2024-01-24 13:49:35,147] [INFO] Target genome list was writen to GCF_000430995.1_TC1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:35,158] [INFO] Task started: fastANI
[2024-01-24 13:49:35,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bacab5a-1dce-4d8b-a790-be70d611c404/GCF_000430995.1_TC1_genomic.fna.gz --refList GCF_000430995.1_TC1_genomic.fna/target_genomes.txt --output GCF_000430995.1_TC1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:49,904] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:49,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged0410c6-7a37-4496-a290-133859bbaab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:49,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged0410c6-7a37-4496-a290-133859bbaab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:49,922] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:49,923] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:49,923] [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
Caloramator fervidus	strain=DSM 5463	GCA_900108045.1	29344	29344	type	True	77.603	177	865	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.5889	89	865	95	below_threshold
Caloramator mitchellensis	strain=VF08	GCA_001440545.1	908809	908809	type	True	77.5711	153	865	95	below_threshold
Caloramator australicus	strain=RC3	GCA_000297115.1	515264	515264	type	True	77.5233	172	865	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.2052	84	865	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	77.0236	94	865	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_001856645.1	1501	1501	type	True	76.9446	91	865	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	76.9265	94	865	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	76.9064	93	865	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	76.8538	95	865	95	below_threshold
Desnuesiella massiliensis	strain=mt10	GCA_001403615.1	1650662	1650662	type	True	76.8399	97	865	95	below_threshold
Clostridium acidisoli	strain=DSM 12555	GCA_900176305.1	91624	91624	type	True	76.6697	69	865	95	below_threshold
Clostridium cylindrosporum	strain=DSM 605	GCA_001047375.1	1495	1495	type	True	76.6351	88	865	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000330945.1	1501	1501	type	True	76.6171	84	865	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_000685115.1	1509	1509	type	True	76.6044	87	865	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	76.5676	93	865	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	76.5541	107	865	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	76.5483	88	865	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	76.5319	72	865	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	76.5257	92	865	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	76.2262	109	865	95	below_threshold
Clostridium intestinale	strain=DSM 6191	GCA_900130055.1	36845	36845	type	True	76.2114	79	865	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_007992895.1	1492	1492	type	True	75.9178	91	865	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	75.8713	90	865	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:49,925] [INFO] DFAST Taxonomy check result was written to GCF_000430995.1_TC1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:49,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:49,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:49,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged0410c6-7a37-4496-a290-133859bbaab6/dqc_reference/checkm_data
[2024-01-24 13:49:49,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:49,958] [INFO] Task started: CheckM
[2024-01-24 13:49:49,958] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000430995.1_TC1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000430995.1_TC1_genomic.fna/checkm_input GCF_000430995.1_TC1_genomic.fna/checkm_result
[2024-01-24 13:50:10,459] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:10,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:10,478] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:10,478] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:10,479] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000430995.1_TC1_genomic.fna/markers.fasta)
[2024-01-24 13:50:10,479] [INFO] Task started: Blastn
[2024-01-24 13:50:10,480] [INFO] Running command: blastn -query GCF_000430995.1_TC1_genomic.fna/markers.fasta -db /var/lib/cwl/stged0410c6-7a37-4496-a290-133859bbaab6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000430995.1_TC1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:11,292] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:11,295] [INFO] Selected 19 target genomes.
[2024-01-24 13:50:11,296] [INFO] Target genome list was writen to GCF_000430995.1_TC1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:11,312] [INFO] Task started: fastANI
[2024-01-24 13:50:11,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bacab5a-1dce-4d8b-a790-be70d611c404/GCF_000430995.1_TC1_genomic.fna.gz --refList GCF_000430995.1_TC1_genomic.fna/target_genomes_gtdb.txt --output GCF_000430995.1_TC1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:21,118] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:21,139] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:21,139] [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_000430995.1	s__Thermobrachium celere	99.9999	857	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Thermobrachium	95.0	98.16	98.16	0.91	0.91	2	conclusive
GCF_900129265.1	s__Caloramator_A proteoclasticus	82.2875	537	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_A	95.0	98.54	98.54	0.90	0.90	2	-
GCF_002327185.1	s__Clostridium chauvoei	77.5559	89	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_000297115.1	s__Caloramator australicus	77.5415	172	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108045.1	s__Caloramator fervidus	77.5413	177	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003288255.1	s__Hathewaya sp003288255	77.2807	84	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167605.1	s__Caloramator_B quimbayensis	77.1453	138	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Caloramator_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020205.1	s__Clostridium_F sporogenes	76.9633	95	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.24	98.80	0.94	0.88	81	-
GCF_001403615.1	s__Desnuesiella massiliensis	76.7503	95	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Desnuesiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001047375.1	s__Clostridium_AB cylindrosporum	76.6698	87	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__Clostridium_AB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002400085.1	s__UBA4839 sp002400085	76.6339	81	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Caloramatoraceae;g__UBA4839	95.0	99.41	99.11	0.85	0.82	15	-
GCF_018917145.1	s__Clostridium_AN bornimense_A	76.5254	85	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AN	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167505.1	s__F0540 sp900167505	76.5097	95	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCF_018918285.1	s__MSJ-11 sp018918285	76.4819	77	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001276215.1	s__Clostridium_F sp001276215	76.2516	90	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_017873215.1	s__Clostridium_AO tetanomorphum	76.2262	109	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	99.85	99.71	0.98	0.97	5	-
GCA_017888565.1	s__Clostridium sp017888565	76.1273	98	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:21,141] [INFO] GTDB search result was written to GCF_000430995.1_TC1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:21,141] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:21,146] [INFO] DFAST_QC result json was written to GCF_000430995.1_TC1_genomic.fna/dqc_result.json
[2024-01-24 13:50:21,146] [INFO] DFAST_QC completed!
[2024-01-24 13:50:21,146] [INFO] Total running time: 0h0m52s