[2024-01-25 18:25:20,912] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:20,914] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:20,914] [INFO] DQC Reference Directory: /var/lib/cwl/stg934c1ad5-0c16-4e9c-95ef-8b55b6873b98/dqc_reference
[2024-01-25 18:25:22,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:22,020] [INFO] Task started: Prodigal
[2024-01-25 18:25:22,020] [INFO] Running command: gunzip -c /var/lib/cwl/stgdff4d823-522a-4f91-ae72-08efdc8b038a/GCF_025152405.1_ASM2515240v1_genomic.fna.gz | prodigal -d GCF_025152405.1_ASM2515240v1_genomic.fna/cds.fna -a GCF_025152405.1_ASM2515240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:27,873] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:27,874] [INFO] Task started: HMMsearch
[2024-01-25 18:25:27,874] [INFO] Running command: hmmsearch --tblout GCF_025152405.1_ASM2515240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg934c1ad5-0c16-4e9c-95ef-8b55b6873b98/dqc_reference/reference_markers.hmm GCF_025152405.1_ASM2515240v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:28,067] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:28,068] [INFO] Found 6/6 markers.
[2024-01-25 18:25:28,089] [INFO] Query marker FASTA was written to GCF_025152405.1_ASM2515240v1_genomic.fna/markers.fasta
[2024-01-25 18:25:28,090] [INFO] Task started: Blastn
[2024-01-25 18:25:28,090] [INFO] Running command: blastn -query GCF_025152405.1_ASM2515240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg934c1ad5-0c16-4e9c-95ef-8b55b6873b98/dqc_reference/reference_markers.fasta -out GCF_025152405.1_ASM2515240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:28,682] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:28,685] [INFO] Selected 13 target genomes.
[2024-01-25 18:25:28,685] [INFO] Target genome list was writen to GCF_025152405.1_ASM2515240v1_genomic.fna/target_genomes.txt
[2024-01-25 18:25:28,696] [INFO] Task started: fastANI
[2024-01-25 18:25:28,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgdff4d823-522a-4f91-ae72-08efdc8b038a/GCF_025152405.1_ASM2515240v1_genomic.fna.gz --refList GCF_025152405.1_ASM2515240v1_genomic.fna/target_genomes.txt --output GCF_025152405.1_ASM2515240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:25:37,097] [INFO] Task succeeded: fastANI
[2024-01-25 18:25:37,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg934c1ad5-0c16-4e9c-95ef-8b55b6873b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:25:37,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg934c1ad5-0c16-4e9c-95ef-8b55b6873b98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:25:37,105] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:25:37,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:25:37,106] [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_025152405.1	46228	46228	type	True	100.0	910	911	95	conclusive
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	99.9289	877	911	95	conclusive
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.162	203	911	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.6021	230	911	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.5844	223	911	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	79.3005	221	911	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.9621	115	911	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	78.8521	101	911	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	78.7739	151	911	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	78.7445	184	911	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	78.3929	178	911	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	78.3866	162	911	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:25:37,108] [INFO] DFAST Taxonomy check result was written to GCF_025152405.1_ASM2515240v1_genomic.fna/tc_result.tsv
[2024-01-25 18:25:37,109] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:25:37,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:25:37,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg934c1ad5-0c16-4e9c-95ef-8b55b6873b98/dqc_reference/checkm_data
[2024-01-25 18:25:37,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:25:37,137] [INFO] Task started: CheckM
[2024-01-25 18:25:37,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025152405.1_ASM2515240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025152405.1_ASM2515240v1_genomic.fna/checkm_input GCF_025152405.1_ASM2515240v1_genomic.fna/checkm_result
[2024-01-25 18:25:59,519] [INFO] Task succeeded: CheckM
[2024-01-25 18:25:59,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:25:59,536] [INFO] ===== Completeness check finished =====
[2024-01-25 18:25:59,537] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:25:59,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025152405.1_ASM2515240v1_genomic.fna/markers.fasta)
[2024-01-25 18:25:59,537] [INFO] Task started: Blastn
[2024-01-25 18:25:59,537] [INFO] Running command: blastn -query GCF_025152405.1_ASM2515240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg934c1ad5-0c16-4e9c-95ef-8b55b6873b98/dqc_reference/reference_markers_gtdb.fasta -out GCF_025152405.1_ASM2515240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:26:00,583] [INFO] Task succeeded: Blastn
[2024-01-25 18:26:00,586] [INFO] Selected 22 target genomes.
[2024-01-25 18:26:00,586] [INFO] Target genome list was writen to GCF_025152405.1_ASM2515240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:26:00,606] [INFO] Task started: fastANI
[2024-01-25 18:26:00,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgdff4d823-522a-4f91-ae72-08efdc8b038a/GCF_025152405.1_ASM2515240v1_genomic.fna.gz --refList GCF_025152405.1_ASM2515240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025152405.1_ASM2515240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:26:13,312] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:13,327] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:26:13,327] [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_000155205.1	s__Mediterraneibacter lactaris	99.9289	877	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	conclusive
GCA_001312505.1	s__Mediterraneibacter faecis	80.81	330	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.72	95.03	0.76	0.67	61	-
GCF_003574295.1	s__Mediterraneibacter_A butyricigenes	80.2627	203	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter_A	95.0	98.15	98.07	0.82	0.80	5	-
GCF_001404875.1	s__Dorea_A longicatena_B	80.0688	184	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCA_003480425.1	s__Schaedlerella sp900066545	79.7184	204	911	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_008121495.1	s__Ruminococcus_B gnavus	79.6436	227	911	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_003435815.1	s__CAG-317 sp000433215	79.1885	195	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCA_004556565.1	s__Schaedlerella sp004556565	78.5125	140	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159505.1	s__Mediterraneibacter ornithocaccae	78.4754	182	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.93	97.52	0.83	0.82	3	-
GCF_002160525.1	s__Mediterraneibacter cottocaccae	78.2991	188	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.81	98.78	0.88	0.86	3	-
GCF_900120155.1	s__Mediterraneibacter sp900120155	78.2612	166	911	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_900544395.1	s__Ruminococcus_B sp900544395	78.1227	171	911	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_904377845.1	s__Mediterraneibacter sp904377845	77.7529	181	911	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_019119745.1	s__Mediterraneibacter gallistercoris	77.7214	140	911	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_900550865.1	s__Dorea_A sp900550865	77.6905	157	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119265.1	s__Mediterraneibacter intestinigallinarum	77.688	159	911	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_019119995.1	s__Mediterraneibacter faecavium	77.6816	168	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.90	99.90	0.92	0.92	2	-
GCA_019115385.1	s__Mediterraneibacter avicola	77.509	144	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.73	98.73	0.86	0.86	2	-
GCA_905209865.1	s__Mediterraneibacter sp900752395	77.4508	154	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.94	99.94	0.94	0.94	2	-
GCA_019120275.1	s__Mediterraneibacter excrementavium	77.3763	144	911	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	77.1892	194	911	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:26:13,328] [INFO] GTDB search result was written to GCF_025152405.1_ASM2515240v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:26:13,329] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:26:13,334] [INFO] DFAST_QC result json was written to GCF_025152405.1_ASM2515240v1_genomic.fna/dqc_result.json
[2024-01-25 18:26:13,334] [INFO] DFAST_QC completed!
[2024-01-25 18:26:13,334] [INFO] Total running time: 0h0m52s