[2023-06-13 18:56:01,752] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:56:01,754] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:56:01,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg408d0f14-24eb-409a-b1f0-4fe6ee2d52b9/dqc_reference
[2023-06-13 18:56:02,880] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:56:02,880] [INFO] Task started: Prodigal
[2023-06-13 18:56:02,881] [INFO] Running command: gunzip -c /var/lib/cwl/stg2210d316-4cb1-4364-a5d3-21dfa0f9ede9/GCA_022786445.1_ASM2278644v1_genomic.fna.gz | prodigal -d GCA_022786445.1_ASM2278644v1_genomic.fna/cds.fna -a GCA_022786445.1_ASM2278644v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:56:08,230] [INFO] Task succeeded: Prodigal
[2023-06-13 18:56:08,230] [INFO] Task started: HMMsearch
[2023-06-13 18:56:08,230] [INFO] Running command: hmmsearch --tblout GCA_022786445.1_ASM2278644v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg408d0f14-24eb-409a-b1f0-4fe6ee2d52b9/dqc_reference/reference_markers.hmm GCA_022786445.1_ASM2278644v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:56:08,419] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:56:08,421] [INFO] Found 6/6 markers.
[2023-06-13 18:56:08,445] [INFO] Query marker FASTA was written to GCA_022786445.1_ASM2278644v1_genomic.fna/markers.fasta
[2023-06-13 18:56:08,445] [INFO] Task started: Blastn
[2023-06-13 18:56:08,445] [INFO] Running command: blastn -query GCA_022786445.1_ASM2278644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg408d0f14-24eb-409a-b1f0-4fe6ee2d52b9/dqc_reference/reference_markers.fasta -out GCA_022786445.1_ASM2278644v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:56:08,964] [INFO] Task succeeded: Blastn
[2023-06-13 18:56:08,971] [INFO] Selected 15 target genomes.
[2023-06-13 18:56:08,972] [INFO] Target genome list was writen to GCA_022786445.1_ASM2278644v1_genomic.fna/target_genomes.txt
[2023-06-13 18:56:08,972] [INFO] Task started: fastANI
[2023-06-13 18:56:08,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg2210d316-4cb1-4364-a5d3-21dfa0f9ede9/GCA_022786445.1_ASM2278644v1_genomic.fna.gz --refList GCA_022786445.1_ASM2278644v1_genomic.fna/target_genomes.txt --output GCA_022786445.1_ASM2278644v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:56:16,401] [INFO] Task succeeded: fastANI
[2023-06-13 18:56:16,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg408d0f14-24eb-409a-b1f0-4fe6ee2d52b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:56:16,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg408d0f14-24eb-409a-b1f0-4fe6ee2d52b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:56:16,412] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:56:16,412] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 18:56:16,412] [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
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	80.722	300	852	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	80.6551	308	852	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	79.8104	185	852	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	79.4576	134	852	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.3095	191	852	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.2734	154	852	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	79.2323	176	852	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	79.0049	187	852	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.9638	190	852	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.9198	194	852	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	78.8234	167	852	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.791	187	852	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	78.518	105	852	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.1476	77	852	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	78.0155	110	852	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 18:56:16,414] [INFO] DFAST Taxonomy check result was written to GCA_022786445.1_ASM2278644v1_genomic.fna/tc_result.tsv
[2023-06-13 18:56:16,420] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:56:16,420] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:56:16,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg408d0f14-24eb-409a-b1f0-4fe6ee2d52b9/dqc_reference/checkm_data
[2023-06-13 18:56:16,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:56:16,450] [INFO] Task started: CheckM
[2023-06-13 18:56:16,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022786445.1_ASM2278644v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022786445.1_ASM2278644v1_genomic.fna/checkm_input GCA_022786445.1_ASM2278644v1_genomic.fna/checkm_result
[2023-06-13 18:56:37,623] [INFO] Task succeeded: CheckM
[2023-06-13 18:56:37,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:56:37,642] [INFO] ===== Completeness check finished =====
[2023-06-13 18:56:37,642] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:56:37,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022786445.1_ASM2278644v1_genomic.fna/markers.fasta)
[2023-06-13 18:56:37,642] [INFO] Task started: Blastn
[2023-06-13 18:56:37,642] [INFO] Running command: blastn -query GCA_022786445.1_ASM2278644v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg408d0f14-24eb-409a-b1f0-4fe6ee2d52b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_022786445.1_ASM2278644v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:56:38,403] [INFO] Task succeeded: Blastn
[2023-06-13 18:56:38,406] [INFO] Selected 19 target genomes.
[2023-06-13 18:56:38,407] [INFO] Target genome list was writen to GCA_022786445.1_ASM2278644v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:56:38,408] [INFO] Task started: fastANI
[2023-06-13 18:56:38,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg2210d316-4cb1-4364-a5d3-21dfa0f9ede9/GCA_022786445.1_ASM2278644v1_genomic.fna.gz --refList GCA_022786445.1_ASM2278644v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022786445.1_ASM2278644v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:56:47,771] [INFO] Task succeeded: fastANI
[2023-06-13 18:56:47,782] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 18:56:47,782] [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_001312505.1	s__Mediterraneibacter faecis	97.3348	704	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	conclusive
GCA_003480425.1	s__Schaedlerella sp900066545	81.2601	255	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.16	96.52	0.81	0.77	11	-
GCF_000155205.1	s__Mediterraneibacter lactaris	80.7628	297	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCF_008121495.1	s__Ruminococcus_B gnavus	79.0114	188	852	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_013300725.1	s__Bariatricus comes_A	78.9823	180	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_002320245.1	s__Schaedlerella sp002320245	78.4384	163	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544395.1	s__Ruminococcus_B sp900544395	78.2552	169	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	99.21	99.21	0.88	0.88	2	-
GCA_019113645.1	s__Mediterraneibacter vanvlietii	77.9374	174	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.04	97.81	0.84	0.83	3	-
GCA_904419285.1	s__Mediterraneibacter caccogallinarum	77.7491	159	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.44	97.89	0.90	0.83	10	-
GCA_904377845.1	s__Mediterraneibacter sp904377845	77.6826	177	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	77.6661	142	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
GCA_900765975.1	s__Schaedlerella sp900765975	77.6362	145	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	77.6207	138	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119675.1	s__Mediterraneibacter faecipullorum	77.5404	148	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761655.1	s__Mediterraneibacter sp900761655	77.4623	97	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228665.1	s__UBA9414 sp003458885	77.3842	122	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCA_018365895.1	s__UBA9414 sp018365895	77.0379	102	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216215.1	s__Bariatricus sp905216215	76.9401	84	852	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 18:56:47,784] [INFO] GTDB search result was written to GCA_022786445.1_ASM2278644v1_genomic.fna/result_gtdb.tsv
[2023-06-13 18:56:47,785] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:56:47,789] [INFO] DFAST_QC result json was written to GCA_022786445.1_ASM2278644v1_genomic.fna/dqc_result.json
[2023-06-13 18:56:47,789] [INFO] DFAST_QC completed!
[2023-06-13 18:56:47,789] [INFO] Total running time: 0h0m46s