[2024-01-24 14:22:32,366] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:32,370] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:32,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg7dc86252-d1e0-4ee8-92a2-49aa127148a0/dqc_reference
[2024-01-24 14:22:33,687] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:33,688] [INFO] Task started: Prodigal
[2024-01-24 14:22:33,689] [INFO] Running command: gunzip -c /var/lib/cwl/stgd88a00a2-85e7-4869-9ae5-0ee7c1676287/GCF_900604355.1_PRJEB27165_genomic.fna.gz | prodigal -d GCF_900604355.1_PRJEB27165_genomic.fna/cds.fna -a GCF_900604355.1_PRJEB27165_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:43,980] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:43,981] [INFO] Task started: HMMsearch
[2024-01-24 14:22:43,981] [INFO] Running command: hmmsearch --tblout GCF_900604355.1_PRJEB27165_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7dc86252-d1e0-4ee8-92a2-49aa127148a0/dqc_reference/reference_markers.hmm GCF_900604355.1_PRJEB27165_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:44,310] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:44,312] [INFO] Found 6/6 markers.
[2024-01-24 14:22:44,354] [INFO] Query marker FASTA was written to GCF_900604355.1_PRJEB27165_genomic.fna/markers.fasta
[2024-01-24 14:22:44,354] [INFO] Task started: Blastn
[2024-01-24 14:22:44,354] [INFO] Running command: blastn -query GCF_900604355.1_PRJEB27165_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dc86252-d1e0-4ee8-92a2-49aa127148a0/dqc_reference/reference_markers.fasta -out GCF_900604355.1_PRJEB27165_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:45,013] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:45,016] [INFO] Selected 25 target genomes.
[2024-01-24 14:22:45,016] [INFO] Target genome list was writen to GCF_900604355.1_PRJEB27165_genomic.fna/target_genomes.txt
[2024-01-24 14:22:45,029] [INFO] Task started: fastANI
[2024-01-24 14:22:45,029] [INFO] Running command: fastANI --query /var/lib/cwl/stgd88a00a2-85e7-4869-9ae5-0ee7c1676287/GCF_900604355.1_PRJEB27165_genomic.fna.gz --refList GCF_900604355.1_PRJEB27165_genomic.fna/target_genomes.txt --output GCF_900604355.1_PRJEB27165_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:01,759] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:01,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7dc86252-d1e0-4ee8-92a2-49aa127148a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:01,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7dc86252-d1e0-4ee8-92a2-49aa127148a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:01,780] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:01,780] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:01,781] [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
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	100.0	1379	1379	95	conclusive
Lachnoclostridium edouardi	strain=Marseille-P3397	GCA_900240245.1	1926283	1926283	type	True	80.2811	67	1379	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	80.1736	52	1379	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	80.065	74	1379	95	below_threshold
Clostridium porci	strain=WCA-389-WT-23D1	GCA_009696375.1	2605778	2605778	type	True	79.9087	57	1379	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	79.8908	58	1379	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	79.8205	89	1379	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.4842	107	1379	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	79.221	103	1379	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	79.1836	69	1379	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	79.1386	284	1379	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.0848	165	1379	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	79.0064	68	1379	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.9876	168	1379	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.7658	155	1379	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	78.6354	69	1379	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.6145	163	1379	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	78.522	131	1379	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	78.2603	71	1379	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	78.2342	142	1379	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	78.1049	63	1379	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.7929	157	1379	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	77.5322	218	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:01,782] [INFO] DFAST Taxonomy check result was written to GCF_900604355.1_PRJEB27165_genomic.fna/tc_result.tsv
[2024-01-24 14:23:01,783] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:01,783] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:01,783] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7dc86252-d1e0-4ee8-92a2-49aa127148a0/dqc_reference/checkm_data
[2024-01-24 14:23:01,784] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:01,824] [INFO] Task started: CheckM
[2024-01-24 14:23:01,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900604355.1_PRJEB27165_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900604355.1_PRJEB27165_genomic.fna/checkm_input GCF_900604355.1_PRJEB27165_genomic.fna/checkm_result
[2024-01-24 14:23:37,309] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:37,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:37,333] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:37,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:37,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900604355.1_PRJEB27165_genomic.fna/markers.fasta)
[2024-01-24 14:23:37,334] [INFO] Task started: Blastn
[2024-01-24 14:23:37,334] [INFO] Running command: blastn -query GCF_900604355.1_PRJEB27165_genomic.fna/markers.fasta -db /var/lib/cwl/stg7dc86252-d1e0-4ee8-92a2-49aa127148a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900604355.1_PRJEB27165_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:38,365] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:38,370] [INFO] Selected 25 target genomes.
[2024-01-24 14:23:38,370] [INFO] Target genome list was writen to GCF_900604355.1_PRJEB27165_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:38,392] [INFO] Task started: fastANI
[2024-01-24 14:23:38,393] [INFO] Running command: fastANI --query /var/lib/cwl/stgd88a00a2-85e7-4869-9ae5-0ee7c1676287/GCF_900604355.1_PRJEB27165_genomic.fna.gz --refList GCF_900604355.1_PRJEB27165_genomic.fna/target_genomes_gtdb.txt --output GCF_900604355.1_PRJEB27165_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:54,367] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:54,387] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:54,388] [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_900604355.1	s__Luxibacter massiliensis	100.0	1379	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Luxibacter	95.0	99.05	99.03	0.91	0.91	3	conclusive
GCA_902362715.1	s__Eubacterium_I sp900066595	80.0888	61	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900240315.1	s__Dorea_B phocaeensis	79.953	86	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_B	95.0	98.22	97.28	0.87	0.81	8	-
GCF_013304445.1	s__Blautia sp900541955	79.7495	55	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.45	99.32	0.89	0.85	6	-
GCF_001404335.1	s__Muricomes contortus_B	79.615	297	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	98.80	98.64	0.86	0.83	8	-
GCF_016902345.1	s__Mediterraneibacter glycyrrhizinilyticus_A	79.0983	130	1379	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_012524165.2	s__Muricomes sp012524165	79.0936	282	1379	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_000155205.1	s__Mediterraneibacter lactaris	79.0828	103	1379	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_018883985.1	s__Ruminococcus_B intestinipullorum	78.7397	76	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149245.1	s__Muricomes oroticus	78.4082	266	1379	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	78.3551	277	1379	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_001487105.1	s__Mediterraneibacter massiliensis	78.1194	141	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.29	98.08	0.94	0.85	4	-
GCF_003149105.1	s__Muricomes contortus_C	78.0366	254	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013911065.1	s__Muricomes sp013911065	77.7663	250	1379	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_004346165.1	s__Muricomes intestini	77.5266	217	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.31	99.22	0.86	0.79	6	-
GCA_910575475.1	s__Schaedlerella sp910575475	77.5087	121	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.35	99.35	0.93	0.93	2	-
GCA_019113645.1	s__Mediterraneibacter vanvlietii	77.2944	121	1379	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_910589385.1	s__Schaedlerella sp910589385	77.2694	113	1379	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_910579015.1	s__Sporofaciens sp910579015	77.126	57	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119995.1	s__Mediterraneibacter faecavium	77.0802	92	1379	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_019119675.1	s__Mediterraneibacter faecipullorum	76.787	86	1379	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_019116885.1	s__Mediterraneibacter pullistercoris	76.7802	90	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.20	99.20	0.93	0.93	2	-
GCA_019119205.1	s__Mediterraneibacter intestinavium	76.6053	83	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.10	98.10	0.78	0.78	2	-
GCA_900765525.1	s__Blautia pullicola	76.3132	52	1379	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia	95.0	99.10	98.67	0.84	0.76	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:54,399] [INFO] GTDB search result was written to GCF_900604355.1_PRJEB27165_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:54,400] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:54,406] [INFO] DFAST_QC result json was written to GCF_900604355.1_PRJEB27165_genomic.fna/dqc_result.json
[2024-01-24 14:23:54,406] [INFO] DFAST_QC completed!
[2024-01-24 14:23:54,407] [INFO] Total running time: 0h1m22s