[2024-01-24 11:26:27,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:27,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:27,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg9facec3d-6419-467d-bf04-0b7e6e3ac762/dqc_reference
[2024-01-24 11:26:29,364] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,365] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,365] [INFO] Running command: gunzip -c /var/lib/cwl/stg13773cbc-de31-4341-b115-32c76a562444/GCF_012524165.2_ASM1252416v2_genomic.fna.gz | prodigal -d GCF_012524165.2_ASM1252416v2_genomic.fna/cds.fna -a GCF_012524165.2_ASM1252416v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:42,053] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:42,053] [INFO] Task started: HMMsearch
[2024-01-24 11:26:42,054] [INFO] Running command: hmmsearch --tblout GCF_012524165.2_ASM1252416v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9facec3d-6419-467d-bf04-0b7e6e3ac762/dqc_reference/reference_markers.hmm GCF_012524165.2_ASM1252416v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:42,414] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:42,415] [INFO] Found 6/6 markers.
[2024-01-24 11:26:42,472] [INFO] Query marker FASTA was written to GCF_012524165.2_ASM1252416v2_genomic.fna/markers.fasta
[2024-01-24 11:26:42,473] [INFO] Task started: Blastn
[2024-01-24 11:26:42,473] [INFO] Running command: blastn -query GCF_012524165.2_ASM1252416v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9facec3d-6419-467d-bf04-0b7e6e3ac762/dqc_reference/reference_markers.fasta -out GCF_012524165.2_ASM1252416v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:43,160] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:43,163] [INFO] Selected 19 target genomes.
[2024-01-24 11:26:43,164] [INFO] Target genome list was writen to GCF_012524165.2_ASM1252416v2_genomic.fna/target_genomes.txt
[2024-01-24 11:26:43,168] [INFO] Task started: fastANI
[2024-01-24 11:26:43,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg13773cbc-de31-4341-b115-32c76a562444/GCF_012524165.2_ASM1252416v2_genomic.fna.gz --refList GCF_012524165.2_ASM1252416v2_genomic.fna/target_genomes.txt --output GCF_012524165.2_ASM1252416v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:54,841] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:54,841] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9facec3d-6419-467d-bf04-0b7e6e3ac762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:54,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9facec3d-6419-467d-bf04-0b7e6e3ac762/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:54,856] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:54,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:54,856] [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
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	100.0	1696	1697	95	conclusive
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.7848	151	1697	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	79.1799	232	1697	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.0531	157	1697	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.933	236	1697	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	78.9207	227	1697	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.9053	232	1697	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.8824	235	1697	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.5707	160	1697	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.4886	159	1697	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	78.1262	254	1697	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.9822	146	1697	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.8053	79	1697	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.7329	97	1697	95	below_threshold
Novisyntrophococcus fermenticellae	strain=JN500902	GCA_018866245.1	2068655	2068655	type	True	77.6156	55	1697	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	77.2586	67	1697	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	77.2247	51	1697	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	77.1172	52	1697	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	76.4068	79	1697	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:54,858] [INFO] DFAST Taxonomy check result was written to GCF_012524165.2_ASM1252416v2_genomic.fna/tc_result.tsv
[2024-01-24 11:26:54,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:54,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:54,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9facec3d-6419-467d-bf04-0b7e6e3ac762/dqc_reference/checkm_data
[2024-01-24 11:26:54,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:54,908] [INFO] Task started: CheckM
[2024-01-24 11:26:54,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012524165.2_ASM1252416v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012524165.2_ASM1252416v2_genomic.fna/checkm_input GCF_012524165.2_ASM1252416v2_genomic.fna/checkm_result
[2024-01-24 11:27:37,716] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:37,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,740] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:37,740] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:37,741] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012524165.2_ASM1252416v2_genomic.fna/markers.fasta)
[2024-01-24 11:27:37,741] [INFO] Task started: Blastn
[2024-01-24 11:27:37,741] [INFO] Running command: blastn -query GCF_012524165.2_ASM1252416v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg9facec3d-6419-467d-bf04-0b7e6e3ac762/dqc_reference/reference_markers_gtdb.fasta -out GCF_012524165.2_ASM1252416v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:38,827] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:38,830] [INFO] Selected 12 target genomes.
[2024-01-24 11:27:38,830] [INFO] Target genome list was writen to GCF_012524165.2_ASM1252416v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:38,839] [INFO] Task started: fastANI
[2024-01-24 11:27:38,839] [INFO] Running command: fastANI --query /var/lib/cwl/stg13773cbc-de31-4341-b115-32c76a562444/GCF_012524165.2_ASM1252416v2_genomic.fna.gz --refList GCF_012524165.2_ASM1252416v2_genomic.fna/target_genomes_gtdb.txt --output GCF_012524165.2_ASM1252416v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:48,607] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:48,624] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:48,624] [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_012524165.2	s__Muricomes sp012524165	100.0	1696	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003149245.1	s__Muricomes oroticus	80.5543	651	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	98.83	98.40	0.88	0.82	5	-
GCF_001028025.1	s__Muricomes fissicatena_A	79.453	425	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.01	99.01	0.90	0.90	3	-
GCF_001404335.1	s__Muricomes contortus_B	79.391	470	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	98.80	98.64	0.86	0.83	8	-
GCA_000403295.2	s__Schaedlerella sp000403295	78.9851	171	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.10	98.10	0.85	0.85	2	-
GCF_008121495.1	s__Ruminococcus_B gnavus	78.9418	235	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCF_900604355.1	s__Luxibacter massiliensis	78.9308	286	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Luxibacter	95.0	99.05	99.03	0.91	0.91	3	-
GCA_000509105.1	s__Muricomes sp000509105	78.9226	431	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.47	98.94	0.90	0.86	4	-
GCA_013911065.1	s__Muricomes sp013911065	78.5568	304	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149105.1	s__Muricomes contortus_C	78.5223	314	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000155205.1	s__Mediterraneibacter lactaris	78.4858	158	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCA_910578865.1	s__CAG-317 sp011960265	77.4496	116	1697	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	99.18	99.18	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:48,626] [INFO] GTDB search result was written to GCF_012524165.2_ASM1252416v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:48,627] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:48,633] [INFO] DFAST_QC result json was written to GCF_012524165.2_ASM1252416v2_genomic.fna/dqc_result.json
[2024-01-24 11:27:48,633] [INFO] DFAST_QC completed!
[2024-01-24 11:27:48,633] [INFO] Total running time: 0h1m21s