[2023-06-12 23:38:00,666] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:38:00,668] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:38:00,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg25f090b4-bea0-40df-89ed-ced401988ad6/dqc_reference
[2023-06-12 23:38:02,923] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:38:02,924] [INFO] Task started: Prodigal
[2023-06-12 23:38:02,925] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0231eec-4fd4-490b-97ee-7be7fcbc1144/GCA_022773025.1_ASM2277302v1_genomic.fna.gz | prodigal -d GCA_022773025.1_ASM2277302v1_genomic.fna/cds.fna -a GCA_022773025.1_ASM2277302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:38:07,927] [INFO] Task succeeded: Prodigal
[2023-06-12 23:38:07,927] [INFO] Task started: HMMsearch
[2023-06-12 23:38:07,927] [INFO] Running command: hmmsearch --tblout GCA_022773025.1_ASM2277302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25f090b4-bea0-40df-89ed-ced401988ad6/dqc_reference/reference_markers.hmm GCA_022773025.1_ASM2277302v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:38:08,238] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:38:08,240] [INFO] Found 6/6 markers.
[2023-06-12 23:38:08,275] [INFO] Query marker FASTA was written to GCA_022773025.1_ASM2277302v1_genomic.fna/markers.fasta
[2023-06-12 23:38:08,275] [INFO] Task started: Blastn
[2023-06-12 23:38:08,275] [INFO] Running command: blastn -query GCA_022773025.1_ASM2277302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f090b4-bea0-40df-89ed-ced401988ad6/dqc_reference/reference_markers.fasta -out GCA_022773025.1_ASM2277302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:38:08,865] [INFO] Task succeeded: Blastn
[2023-06-12 23:38:08,870] [INFO] Selected 30 target genomes.
[2023-06-12 23:38:08,870] [INFO] Target genome list was writen to GCA_022773025.1_ASM2277302v1_genomic.fna/target_genomes.txt
[2023-06-12 23:38:08,881] [INFO] Task started: fastANI
[2023-06-12 23:38:08,881] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0231eec-4fd4-490b-97ee-7be7fcbc1144/GCA_022773025.1_ASM2277302v1_genomic.fna.gz --refList GCA_022773025.1_ASM2277302v1_genomic.fna/target_genomes.txt --output GCA_022773025.1_ASM2277302v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:38:27,702] [INFO] Task succeeded: fastANI
[2023-06-12 23:38:27,702] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25f090b4-bea0-40df-89ed-ced401988ad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:38:27,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25f090b4-bea0-40df-89ed-ced401988ad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:38:27,722] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:38:27,722] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:38:27,722] [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 frigidicarnis	strain=DSM 12271	GCA_900111985.1	84698	84698	type	True	77.5262	151	997	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.1438	127	997	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	77.1387	125	997	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.1227	125	997	95	below_threshold
Clostridium amylolyticum	strain=DSM 21864	GCA_900142075.1	1121298	1121298	type	True	77.0867	91	997	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.973	117	997	95	below_threshold
Clostridium hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	76.9443	159	997	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	76.9156	103	997	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.8686	112	997	95	below_threshold
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	76.8255	99	997	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	76.7866	103	997	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	76.6308	98	997	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	76.5897	84	997	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	76.5859	111	997	95	below_threshold
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	76.5753	87	997	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	76.4914	103	997	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_002006445.1	1520	1520	suspected-type	True	76.3929	99	997	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	76.377	104	997	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.3503	80	997	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.1637	109	997	95	below_threshold
Clostridium acidisoli	strain=DSM 12555	GCA_900176305.1	91624	91624	type	True	76.1624	65	997	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.1038	90	997	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.0815	89	997	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	76.0531	115	997	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	76.0529	115	997	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:38:27,724] [INFO] DFAST Taxonomy check result was written to GCA_022773025.1_ASM2277302v1_genomic.fna/tc_result.tsv
[2023-06-12 23:38:27,726] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:38:27,726] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:38:27,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25f090b4-bea0-40df-89ed-ced401988ad6/dqc_reference/checkm_data
[2023-06-12 23:38:27,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:38:27,762] [INFO] Task started: CheckM
[2023-06-12 23:38:27,762] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022773025.1_ASM2277302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022773025.1_ASM2277302v1_genomic.fna/checkm_input GCA_022773025.1_ASM2277302v1_genomic.fna/checkm_result
[2023-06-12 23:38:49,878] [INFO] Task succeeded: CheckM
[2023-06-12 23:38:49,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:38:49,912] [INFO] ===== Completeness check finished =====
[2023-06-12 23:38:49,914] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:38:49,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022773025.1_ASM2277302v1_genomic.fna/markers.fasta)
[2023-06-12 23:38:49,915] [INFO] Task started: Blastn
[2023-06-12 23:38:49,915] [INFO] Running command: blastn -query GCA_022773025.1_ASM2277302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25f090b4-bea0-40df-89ed-ced401988ad6/dqc_reference/reference_markers_gtdb.fasta -out GCA_022773025.1_ASM2277302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:38:50,676] [INFO] Task succeeded: Blastn
[2023-06-12 23:38:50,682] [INFO] Selected 24 target genomes.
[2023-06-12 23:38:50,682] [INFO] Target genome list was writen to GCA_022773025.1_ASM2277302v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:38:50,696] [INFO] Task started: fastANI
[2023-06-12 23:38:50,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0231eec-4fd4-490b-97ee-7be7fcbc1144/GCA_022773025.1_ASM2277302v1_genomic.fna.gz --refList GCA_022773025.1_ASM2277302v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022773025.1_ASM2277302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:39:05,623] [INFO] Task succeeded: fastANI
[2023-06-12 23:39:05,643] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-12 23:39:05,643] [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_000424205.1	s__Clostridium_X cadaveris	86.8897	802	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	99.52	99.40	0.92	0.82	7	-
GCA_002423705.1	s__Clostridium_X sp002423705	78.3041	272	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111985.1	s__Clostridium_Z frigidicarnis	77.5309	150	997	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	-
GCA_900539375.1	s__Clostridium sp900539375	77.2335	90	997	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_900129365.1	s__Clostridium_AH fallax	77.1194	126	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900086595.1	s__Clostridium nigeriense	77.0995	126	997	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_004794105.1	s__Clostridium sartagoforme_B	76.9921	120	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCF_018918055.1	s__Clostridium sp018918055	76.9491	79	997	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	76.9443	159	997	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_009928445.1	s__Clostridium_AR sp009928445	76.9061	101	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	76.9046	120	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	99.33	97.98	0.97	0.93	4	-
GCF_014836325.1	s__Clostridium sp014836325	76.8908	112	997	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_009295725.1	s__Clostridium_P tarantellae	76.5859	111	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016316925.1	s__Clostridium_AM aciditolerans	76.5507	88	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	95.27	95.27	0.80	0.80	2	-
GCA_009738435.1	s__Clostridium_H bovifaecis	76.5347	69	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184255.1	s__Haloimpatiens massiliensis	76.4914	103	997	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_018223745.1	s__Clostridium beijerinckii	76.377	104	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	-
GCF_002008345.1	s__Clostridium_F tepidum	76.1998	117	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_002006355.1	s__Clostridium_S felsineum	76.0698	87	997	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	-
GCF_001276215.1	s__Clostridium_F sp001276215	76.047	98	997	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_001276985.1	s__Clostridium_F botulinum	75.9885	111	997	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
--------------------------------------------------------------------------------
[2023-06-12 23:39:05,645] [INFO] GTDB search result was written to GCA_022773025.1_ASM2277302v1_genomic.fna/result_gtdb.tsv
[2023-06-12 23:39:05,646] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:39:05,651] [INFO] DFAST_QC result json was written to GCA_022773025.1_ASM2277302v1_genomic.fna/dqc_result.json
[2023-06-12 23:39:05,651] [INFO] DFAST_QC completed!
[2023-06-12 23:39:05,651] [INFO] Total running time: 0h1m5s