[2024-01-25 20:21:50,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:50,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:50,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ccd7fc2-fe20-4f02-b46a-79488b5c3435/dqc_reference
[2024-01-25 20:21:51,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:51,741] [INFO] Task started: Prodigal
[2024-01-25 20:21:51,741] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d76f742-2986-47d8-b88e-42e670a5ee02/GCF_025567345.1_ASM2556734v1_genomic.fna.gz | prodigal -d GCF_025567345.1_ASM2556734v1_genomic.fna/cds.fna -a GCF_025567345.1_ASM2556734v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:57,740] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:57,740] [INFO] Task started: HMMsearch
[2024-01-25 20:21:57,740] [INFO] Running command: hmmsearch --tblout GCF_025567345.1_ASM2556734v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ccd7fc2-fe20-4f02-b46a-79488b5c3435/dqc_reference/reference_markers.hmm GCF_025567345.1_ASM2556734v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:57,961] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:57,962] [INFO] Found 6/6 markers.
[2024-01-25 20:21:57,985] [INFO] Query marker FASTA was written to GCF_025567345.1_ASM2556734v1_genomic.fna/markers.fasta
[2024-01-25 20:21:57,985] [INFO] Task started: Blastn
[2024-01-25 20:21:57,985] [INFO] Running command: blastn -query GCF_025567345.1_ASM2556734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ccd7fc2-fe20-4f02-b46a-79488b5c3435/dqc_reference/reference_markers.fasta -out GCF_025567345.1_ASM2556734v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:58,575] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:58,578] [INFO] Selected 24 target genomes.
[2024-01-25 20:21:58,578] [INFO] Target genome list was writen to GCF_025567345.1_ASM2556734v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:58,601] [INFO] Task started: fastANI
[2024-01-25 20:21:58,602] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d76f742-2986-47d8-b88e-42e670a5ee02/GCF_025567345.1_ASM2556734v1_genomic.fna.gz --refList GCF_025567345.1_ASM2556734v1_genomic.fna/target_genomes.txt --output GCF_025567345.1_ASM2556734v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:11,178] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:11,178] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ccd7fc2-fe20-4f02-b46a-79488b5c3435/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:11,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ccd7fc2-fe20-4f02-b46a-79488b5c3435/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:11,188] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:22:11,188] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:22:11,188] [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
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	80.3327	179	966	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	80.3196	180	966	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	79.8042	145	966	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	79.5323	65	966	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	79.5001	67	966	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	79.2134	67	966	95	below_threshold
Coprococcus catus	strain=ATCC 27761	GCA_025289135.1	116085	116085	suspected-type	True	78.9423	67	966	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.7559	90	966	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	78.6984	79	966	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.4981	87	966	95	below_threshold
Jutongia hominis	strain=BX3	GCA_014384965.1	2763664	2763664	type	True	78.4236	69	966	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.293	63	966	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.4217	60	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:11,189] [INFO] DFAST Taxonomy check result was written to GCF_025567345.1_ASM2556734v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:11,190] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:11,190] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:11,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ccd7fc2-fe20-4f02-b46a-79488b5c3435/dqc_reference/checkm_data
[2024-01-25 20:22:11,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:11,222] [INFO] Task started: CheckM
[2024-01-25 20:22:11,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567345.1_ASM2556734v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567345.1_ASM2556734v1_genomic.fna/checkm_input GCF_025567345.1_ASM2556734v1_genomic.fna/checkm_result
[2024-01-25 20:22:34,309] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:34,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:34,328] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:34,329] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:34,329] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567345.1_ASM2556734v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:34,330] [INFO] Task started: Blastn
[2024-01-25 20:22:34,330] [INFO] Running command: blastn -query GCF_025567345.1_ASM2556734v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ccd7fc2-fe20-4f02-b46a-79488b5c3435/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567345.1_ASM2556734v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:35,386] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:35,389] [INFO] Selected 10 target genomes.
[2024-01-25 20:22:35,389] [INFO] Target genome list was writen to GCF_025567345.1_ASM2556734v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:35,398] [INFO] Task started: fastANI
[2024-01-25 20:22:35,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d76f742-2986-47d8-b88e-42e670a5ee02/GCF_025567345.1_ASM2556734v1_genomic.fna.gz --refList GCF_025567345.1_ASM2556734v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567345.1_ASM2556734v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:40,771] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:40,778] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:40,778] [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_003461625.1	s__Coprococcus sp900066115	98.7392	821	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.16	97.77	0.91	0.89	23	conclusive
GCF_000154245.1	s__Coprococcus sp000154245	94.3673	745	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.94	98.58	0.93	0.88	6	-
GCA_002437435.1	s__Coprococcus sp002437435	90.0739	665	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154425.1	s__Coprococcus eutactus	80.3007	180	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.55	98.02	0.90	0.86	8	-
GCF_003482105.1	s__Coprococcus sp000433075	80.1315	206	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	99.05	98.02	0.96	0.92	5	-
GCA_900761435.1	s__Coprococcus sp900761435	79.5816	308	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548215.1	s__Coprococcus sp900548215	78.6238	137	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.00	97.92	0.89	0.88	3	-
GCA_900557435.1	s__Coprococcus sp900557435	78.2785	89	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935345.1	s__Coprococcus sp017935345	77.9787	176	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296785.1	s__Coprococcus sp016296785	77.7875	136	966	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:40,780] [INFO] GTDB search result was written to GCF_025567345.1_ASM2556734v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:40,780] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:40,783] [INFO] DFAST_QC result json was written to GCF_025567345.1_ASM2556734v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:40,783] [INFO] DFAST_QC completed!
[2024-01-25 20:22:40,783] [INFO] Total running time: 0h0m50s