[2024-01-24 13:32:34,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,075] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg460b6f7d-7c9c-494b-8d69-44628c1ece4f/dqc_reference
[2024-01-24 13:32:35,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:35,488] [INFO] Task started: Prodigal
[2024-01-24 13:32:35,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e67252c-02c0-48c7-b34b-6a38e769cacc/GCF_009696465.1_ASM969646v1_genomic.fna.gz | prodigal -d GCF_009696465.1_ASM969646v1_genomic.fna/cds.fna -a GCF_009696465.1_ASM969646v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:40,907] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:40,907] [INFO] Task started: HMMsearch
[2024-01-24 13:32:40,907] [INFO] Running command: hmmsearch --tblout GCF_009696465.1_ASM969646v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg460b6f7d-7c9c-494b-8d69-44628c1ece4f/dqc_reference/reference_markers.hmm GCF_009696465.1_ASM969646v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:41,304] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:41,306] [INFO] Found 6/6 markers.
[2024-01-24 13:32:41,350] [INFO] Query marker FASTA was written to GCF_009696465.1_ASM969646v1_genomic.fna/markers.fasta
[2024-01-24 13:32:41,350] [INFO] Task started: Blastn
[2024-01-24 13:32:41,350] [INFO] Running command: blastn -query GCF_009696465.1_ASM969646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg460b6f7d-7c9c-494b-8d69-44628c1ece4f/dqc_reference/reference_markers.fasta -out GCF_009696465.1_ASM969646v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:41,970] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:41,973] [INFO] Selected 23 target genomes.
[2024-01-24 13:32:41,974] [INFO] Target genome list was writen to GCF_009696465.1_ASM969646v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:41,982] [INFO] Task started: fastANI
[2024-01-24 13:32:41,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e67252c-02c0-48c7-b34b-6a38e769cacc/GCF_009696465.1_ASM969646v1_genomic.fna.gz --refList GCF_009696465.1_ASM969646v1_genomic.fna/target_genomes.txt --output GCF_009696465.1_ASM969646v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:56,879] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:56,880] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg460b6f7d-7c9c-494b-8d69-44628c1ece4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:56,880] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg460b6f7d-7c9c-494b-8d69-44628c1ece4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:56,897] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:56,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:56,898] [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
Inconstantimicrobium porci	strain=WCA-383-APC-5B	GCA_009696465.1	2652291	2652291	type	True	100.0	1024	1029	95	conclusive
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	77.8431	118	1029	95	below_threshold
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	77.5994	126	1029	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	77.4717	106	1029	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.4003	115	1029	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	77.3536	118	1029	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.2437	120	1029	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	77.0985	105	1029	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	77.0741	123	1029	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	77.0114	143	1029	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	76.961	136	1029	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	76.9205	139	1029	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.8928	83	1029	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.8795	109	1029	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.8294	133	1029	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.5712	100	1029	95	below_threshold
Clostridium gasigenes	strain=DSM 12272	GCA_900104115.1	94869	94869	type	True	76.5628	94	1029	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.3121	84	1029	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	76.2803	102	1029	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	76.1064	76	1029	95	below_threshold
Romboutsia timonensis	strain=Marseille-P326	GCA_900106845.1	1776391	1776391	type	True	75.7259	59	1029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:56,900] [INFO] DFAST Taxonomy check result was written to GCF_009696465.1_ASM969646v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:56,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:56,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:56,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg460b6f7d-7c9c-494b-8d69-44628c1ece4f/dqc_reference/checkm_data
[2024-01-24 13:32:56,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:56,944] [INFO] Task started: CheckM
[2024-01-24 13:32:56,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696465.1_ASM969646v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696465.1_ASM969646v1_genomic.fna/checkm_input GCF_009696465.1_ASM969646v1_genomic.fna/checkm_result
[2024-01-24 13:33:22,000] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:22,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:22,027] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:22,027] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:22,027] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696465.1_ASM969646v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:22,028] [INFO] Task started: Blastn
[2024-01-24 13:33:22,028] [INFO] Running command: blastn -query GCF_009696465.1_ASM969646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg460b6f7d-7c9c-494b-8d69-44628c1ece4f/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696465.1_ASM969646v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:22,822] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:22,826] [INFO] Selected 27 target genomes.
[2024-01-24 13:33:22,826] [INFO] Target genome list was writen to GCF_009696465.1_ASM969646v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:22,903] [INFO] Task started: fastANI
[2024-01-24 13:33:22,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e67252c-02c0-48c7-b34b-6a38e769cacc/GCF_009696465.1_ASM969646v1_genomic.fna.gz --refList GCF_009696465.1_ASM969646v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696465.1_ASM969646v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:39,902] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:39,922] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:39,923] [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_009696465.1	s__Inconstantimicrobium porci	100.0	1024	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Inconstantimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000013285.1	s__Clostridium_P perfringens	77.8431	118	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.05	95.74	0.91	0.81	315	-
GCF_000789395.1	s__Clostridium baratii	77.6439	134	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCF_900116755.1	s__Clostridium sp900116755	77.4894	140	1029	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_015058525.1	s__Clostridium butyricum_A	77.4799	107	1029	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_002327185.1	s__Clostridium chauvoei	77.4113	114	1029	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_012519155.1	s__Clostridium sp012519155	77.2893	93	1029	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_900086595.1	s__Clostridium nigeriense	77.2671	119	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.98	98.98	0.91	0.91	2	-
GCF_016907995.1	s__Clostridium sardiniense	77.1169	121	1029	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_001403635.1	s__Clostridium_P massiliamazoniense	77.0835	102	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112485.1	s__Clostridium uliginosum	77.0802	118	1029	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_015670405.1	s__Clostridium sp015670405	77.0319	136	1029	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_900141845.1	s__Clostridium_AG cavendishii	77.0114	143	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000320405.1	s__Clostridium celatum	76.961	136	1029	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_000577815.1	s__Clostridium saudiense	76.9551	138	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.39	99.24	0.89	0.87	14	-
GCA_900540255.1	s__Clostridium sp900540255	76.9393	124	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
GCA_900766315.1	s__Clostridium sp900766315	76.8269	149	1029	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_900759995.1	s__Clostridium sp900759995	76.8124	106	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.46	98.18	0.80	0.79	3	-
GCA_000435835.1	s__Clostridium sp000435835	76.7669	112	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.44	99.22	0.92	0.88	4	-
GCF_900104115.1	s__Clostridium gasigenes	76.5845	93	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.21	97.55	0.90	0.87	10	-
GCF_002006355.1	s__Clostridium_S felsineum	76.5575	88	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	98.29	98.24	0.88	0.87	4	-
GCA_018372555.1	s__Clostridium sp018372555	76.4416	91	1029	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_900130055.1	s__Clostridium_T intestinale	76.399	109	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_T	95.0	95.87	95.52	0.87	0.83	4	-
GCF_002760435.1	s__Clostridium sp002760435	76.2369	119	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_001243045.1	s__Clostridium_F niameyense	76.0632	75	1029	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.56	99.11	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:39,925] [INFO] GTDB search result was written to GCF_009696465.1_ASM969646v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:39,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:39,930] [INFO] DFAST_QC result json was written to GCF_009696465.1_ASM969646v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:39,930] [INFO] DFAST_QC completed!
[2024-01-24 13:33:39,930] [INFO] Total running time: 0h1m6s