[2024-01-25 17:34:07,124] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,129] [INFO] DQC Reference Directory: /var/lib/cwl/stg961f07a0-2829-4510-91d7-6380f24564ba/dqc_reference
[2024-01-25 17:34:09,030] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,031] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,031] [INFO] Running command: gunzip -c /var/lib/cwl/stge3f9e9ea-1703-4aaa-86d3-6f2def787bbc/GCF_030815255.1_ASM3081525v1_genomic.fna.gz | prodigal -d GCF_030815255.1_ASM3081525v1_genomic.fna/cds.fna -a GCF_030815255.1_ASM3081525v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:12,837] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:12,838] [INFO] Task started: HMMsearch
[2024-01-25 17:34:12,838] [INFO] Running command: hmmsearch --tblout GCF_030815255.1_ASM3081525v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg961f07a0-2829-4510-91d7-6380f24564ba/dqc_reference/reference_markers.hmm GCF_030815255.1_ASM3081525v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:13,208] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:13,209] [INFO] Found 6/6 markers.
[2024-01-25 17:34:13,234] [INFO] Query marker FASTA was written to GCF_030815255.1_ASM3081525v1_genomic.fna/markers.fasta
[2024-01-25 17:34:13,234] [INFO] Task started: Blastn
[2024-01-25 17:34:13,234] [INFO] Running command: blastn -query GCF_030815255.1_ASM3081525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg961f07a0-2829-4510-91d7-6380f24564ba/dqc_reference/reference_markers.fasta -out GCF_030815255.1_ASM3081525v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:14,717] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:14,721] [INFO] Selected 22 target genomes.
[2024-01-25 17:34:14,721] [INFO] Target genome list was writen to GCF_030815255.1_ASM3081525v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:14,805] [INFO] Task started: fastANI
[2024-01-25 17:34:14,805] [INFO] Running command: fastANI --query /var/lib/cwl/stge3f9e9ea-1703-4aaa-86d3-6f2def787bbc/GCF_030815255.1_ASM3081525v1_genomic.fna.gz --refList GCF_030815255.1_ASM3081525v1_genomic.fna/target_genomes.txt --output GCF_030815255.1_ASM3081525v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:27,636] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:27,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg961f07a0-2829-4510-91d7-6380f24564ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:27,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg961f07a0-2829-4510-91d7-6380f24564ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:27,648] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:34:27,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:34:27,649] [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
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	78.4612	307	995	95	below_threshold
Hathewaya massiliensis	strain=Marseille-P3545	GCA_902143515.1	1964382	1964382	type	True	78.4051	309	995	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	78.0225	182	995	95	below_threshold
Clostridium collagenovorans	strain=DSM 3089	GCA_900130005.1	29357	29357	type	True	77.3135	190	995	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	77.1023	184	995	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	76.7958	192	995	95	below_threshold
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	76.7661	201	995	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	76.7299	162	995	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	76.5301	149	995	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	76.4114	166	995	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	76.3916	129	995	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	76.3805	152	995	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.1973	154	995	95	below_threshold
Clostridium algidicarnis	strain=DSM 15099	GCA_002934235.1	37659	37659	type	True	76.1633	115	995	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	76.0409	137	995	95	below_threshold
Clostridium ljungdahlii	strain=DSM 13528	GCA_000143685.1	1538	1538	suspected-type	True	76.0028	113	995	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	75.8776	150	995	95	below_threshold
Clostridium kluyveri	strain=DSM 555	GCA_000016505.1	1534	1534	type	True	75.7487	80	995	95	below_threshold
Clostridium kluyveri	strain=NBRC 12016	GCA_000010265.1	1534	1534	type	True	75.7487	80	995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:27,653] [INFO] DFAST Taxonomy check result was written to GCF_030815255.1_ASM3081525v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:27,654] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:27,654] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:27,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg961f07a0-2829-4510-91d7-6380f24564ba/dqc_reference/checkm_data
[2024-01-25 17:34:27,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:27,687] [INFO] Task started: CheckM
[2024-01-25 17:34:27,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030815255.1_ASM3081525v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030815255.1_ASM3081525v1_genomic.fna/checkm_input GCF_030815255.1_ASM3081525v1_genomic.fna/checkm_result
[2024-01-25 17:34:45,576] [INFO] Task succeeded: CheckM
[2024-01-25 17:34:45,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:34:45,603] [INFO] ===== Completeness check finished =====
[2024-01-25 17:34:45,603] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:34:45,603] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030815255.1_ASM3081525v1_genomic.fna/markers.fasta)
[2024-01-25 17:34:45,603] [INFO] Task started: Blastn
[2024-01-25 17:34:45,604] [INFO] Running command: blastn -query GCF_030815255.1_ASM3081525v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg961f07a0-2829-4510-91d7-6380f24564ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_030815255.1_ASM3081525v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:46,904] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:46,907] [INFO] Selected 28 target genomes.
[2024-01-25 17:34:46,907] [INFO] Target genome list was writen to GCF_030815255.1_ASM3081525v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:34:46,945] [INFO] Task started: fastANI
[2024-01-25 17:34:46,945] [INFO] Running command: fastANI --query /var/lib/cwl/stge3f9e9ea-1703-4aaa-86d3-6f2def787bbc/GCF_030815255.1_ASM3081525v1_genomic.fna.gz --refList GCF_030815255.1_ASM3081525v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030815255.1_ASM3081525v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:35:02,387] [INFO] Task succeeded: fastANI
[2024-01-25 17:35:02,400] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:35:02,400] [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_003288255.1	s__Hathewaya sp003288255	98.2504	873	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_901482605.1	s__Hathewaya histolytica	78.4612	307	995	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_902143515.1	s__Hathewaya massiliensis	78.4085	308	995	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_900130005.1	s__Clostridium_D collagenovorans	77.284	192	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614235.1	s__Clostridium_H haemolyticum	77.1487	160	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.44	97.38	0.90	0.84	13	-
GCF_900184255.1	s__Haloimpatiens massiliensis	77.1023	184	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285575.1	s__Clostridium_J senegalense	76.7716	194	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	97.19	95.52	0.93	0.91	5	-
GCF_000612845.1	s__Clostridium_J ihumii	76.7547	202	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900176615.1	s__Clostridium_H massiliodielmoense	76.7021	164	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.64	96.44	0.92	0.87	5	-
GCA_017435645.1	s__Clostridium sp017435645	76.4786	68	995	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	76.3786	130	995	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_000789395.1	s__Clostridium baratii	76.2789	120	995	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_018918285.1	s__MSJ-11 sp018918285	76.2515	133	995	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_018917145.1	s__Clostridium_AN bornimense_A	76.2045	115	995	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_002934235.1	s__Clostridium_L algidicarnis	76.1633	115	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	97.66	96.15	0.89	0.86	14	-
GCA_900539375.1	s__Clostridium sp900539375	76.0414	137	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.09	99.02	0.89	0.86	4	-
GCF_000577815.1	s__Clostridium saudiense	76.0409	137	995	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_001675165.1	s__Clostridium_B ragsdalei	75.9677	100	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	98.18	98.18	0.88	0.88	2	-
GCA_902785295.1	s__Clostridium sp902785295	75.8973	113	995	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_009928485.1	s__Clostridium sp009928485	75.8681	141	995	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_000686705.1	s__Clostridium_Z hydrogeniformans	75.8668	154	995	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129265.1	s__Caloramator_A proteoclasticus	75.6701	63	995	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:35:02,401] [INFO] GTDB search result was written to GCF_030815255.1_ASM3081525v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:35:02,402] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:35:02,405] [INFO] DFAST_QC result json was written to GCF_030815255.1_ASM3081525v1_genomic.fna/dqc_result.json
[2024-01-25 17:35:02,405] [INFO] DFAST_QC completed!
[2024-01-25 17:35:02,406] [INFO] Total running time: 0h0m55s