[2024-01-24 11:26:28,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,110] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,111] [INFO] DQC Reference Directory: /var/lib/cwl/stgf25e18ce-0a75-4824-b63d-884e451e99dc/dqc_reference
[2024-01-24 11:26:29,372] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,375] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,375] [INFO] Running command: gunzip -c /var/lib/cwl/stge2162dc8-221f-4ca7-87ee-46392f03b871/GCF_014385095.1_ASM1438509v1_genomic.fna.gz | prodigal -d GCF_014385095.1_ASM1438509v1_genomic.fna/cds.fna -a GCF_014385095.1_ASM1438509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:37,481] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:37,482] [INFO] Task started: HMMsearch
[2024-01-24 11:26:37,482] [INFO] Running command: hmmsearch --tblout GCF_014385095.1_ASM1438509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf25e18ce-0a75-4824-b63d-884e451e99dc/dqc_reference/reference_markers.hmm GCF_014385095.1_ASM1438509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:37,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:37,755] [INFO] Found 6/6 markers.
[2024-01-24 11:26:37,778] [INFO] Query marker FASTA was written to GCF_014385095.1_ASM1438509v1_genomic.fna/markers.fasta
[2024-01-24 11:26:37,779] [INFO] Task started: Blastn
[2024-01-24 11:26:37,779] [INFO] Running command: blastn -query GCF_014385095.1_ASM1438509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf25e18ce-0a75-4824-b63d-884e451e99dc/dqc_reference/reference_markers.fasta -out GCF_014385095.1_ASM1438509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:38,535] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:38,544] [INFO] Selected 23 target genomes.
[2024-01-24 11:26:38,545] [INFO] Target genome list was writen to GCF_014385095.1_ASM1438509v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:38,555] [INFO] Task started: fastANI
[2024-01-24 11:26:38,555] [INFO] Running command: fastANI --query /var/lib/cwl/stge2162dc8-221f-4ca7-87ee-46392f03b871/GCF_014385095.1_ASM1438509v1_genomic.fna.gz --refList GCF_014385095.1_ASM1438509v1_genomic.fna/target_genomes.txt --output GCF_014385095.1_ASM1438509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:52,899] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:52,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf25e18ce-0a75-4824-b63d-884e451e99dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:52,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf25e18ce-0a75-4824-b63d-884e451e99dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:52,914] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:52,914] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:52,914] [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
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	79.8081	75	844	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	79.7773	57	844	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_025146135.1	169435	169435	type	True	79.4142	53	844	95	below_threshold
Provencibacterium massiliense	strain=Marseille-P2780	GCA_900169495.1	1841868	1841868	type	True	78.7029	150	844	95	below_threshold
Angelakisella massiliensis	strain=Marseille-P3217	GCA_900104675.1	1871018	1871018	type	True	78.5013	120	844	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	78.3075	158	844	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	78.2972	146	844	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.2857	93	844	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	78.2461	87	844	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	78.0078	61	844	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.9288	77	844	95	below_threshold
Phocea massiliensis	strain=Marseille-P2769	GCA_900104615.1	1841867	1841867	type	True	77.8463	119	844	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.8027	70	844	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.65	141	844	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.4447	93	844	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.3984	90	844	95	below_threshold
Neglectibacter timonensis	strain=SN17	GCA_900048895.1	1776382	1776382	type	True	77.2784	56	844	95	below_threshold
Feifania hominis	strain=BX7	GCA_014384765.1	2763660	2763660	type	True	77.0272	53	844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:52,916] [INFO] DFAST Taxonomy check result was written to GCF_014385095.1_ASM1438509v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:52,916] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:52,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:52,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf25e18ce-0a75-4824-b63d-884e451e99dc/dqc_reference/checkm_data
[2024-01-24 11:26:52,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:52,946] [INFO] Task started: CheckM
[2024-01-24 11:26:52,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385095.1_ASM1438509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385095.1_ASM1438509v1_genomic.fna/checkm_input GCF_014385095.1_ASM1438509v1_genomic.fna/checkm_result
[2024-01-24 11:27:21,664] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:21,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:21,686] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:21,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:21,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385095.1_ASM1438509v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:21,687] [INFO] Task started: Blastn
[2024-01-24 11:27:21,687] [INFO] Running command: blastn -query GCF_014385095.1_ASM1438509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf25e18ce-0a75-4824-b63d-884e451e99dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385095.1_ASM1438509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:22,895] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:22,900] [INFO] Selected 20 target genomes.
[2024-01-24 11:27:22,900] [INFO] Target genome list was writen to GCF_014385095.1_ASM1438509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:22,928] [INFO] Task started: fastANI
[2024-01-24 11:27:22,928] [INFO] Running command: fastANI --query /var/lib/cwl/stge2162dc8-221f-4ca7-87ee-46392f03b871/GCF_014385095.1_ASM1438509v1_genomic.fna.gz --refList GCF_014385095.1_ASM1438509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014385095.1_ASM1438509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:30,779] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:30,800] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:30,800] [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_014385095.1	s__Pararuminococcus sp014385095	100.0	843	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pararuminococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_904419775.1	s__Pararuminococcus gallinarum	79.6005	304	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Pararuminococcus	95.0	98.53	98.53	0.92	0.92	2	-
GCF_900289145.1	s__Neobittarella massiliensis	77.7469	113	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Neobittarella	95.0	98.40	98.40	0.93	0.93	4	-
GCF_900199635.1	s__Anaerotruncus massiliensis	77.65	141	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCF_904387055.1	s__Heteroruminococcus faecigallinarum	77.4499	116	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Heteroruminococcus	95.0	99.97	99.97	0.96	0.96	2	-
GCA_004340125.1	s__Harryflintia acetispora	77.3492	139	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Harryflintia	95.0	98.73	98.54	0.92	0.90	6	-
GCF_904398325.1	s__Neoruminococcus faecicola	77.2317	98	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Neoruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000820765.1	s__Soleaferrea massiliensis	77.176	80	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Soleaferrea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904419105.1	s__Avimicrobium faecavium	77.1305	69	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761965.1	s__Avimicrobium sp900761965	77.0466	54	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	98.03	98.03	0.92	0.92	2	-
GCA_910578255.1	s__UBA3818 sp910578255	77.0083	61	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__UBA3818	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543555.1	s__Acutalibacter stercoravium	76.964	68	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Acutalibacter	95.0	98.18	97.66	0.89	0.84	11	-
GCF_904397835.1	s__Aristotella avistercoris	76.9512	97	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Aristotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420015.1	s__JAGZMM01 sp904420015	76.9107	87	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__JAGZMM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904420045.1	s__Metaruminococcus caecorum	76.9073	101	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Metaruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904420585.1	s__Howiella intestinavium	76.8881	101	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Howiella	95.0	98.63	98.63	0.91	0.91	2	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	76.7924	110	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.88	99.88	0.94	0.94	2	-
GCA_900761355.1	s__Avimonas intestinalis	76.1899	72	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	99.06	98.52	0.89	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,802] [INFO] GTDB search result was written to GCF_014385095.1_ASM1438509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:30,803] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:30,807] [INFO] DFAST_QC result json was written to GCF_014385095.1_ASM1438509v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:30,808] [INFO] DFAST_QC completed!
[2024-01-24 11:27:30,808] [INFO] Total running time: 0h1m3s