[2024-01-25 18:07:05,715] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:05,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:05,717] [INFO] DQC Reference Directory: /var/lib/cwl/stgb2222983-f2b3-46d9-9851-fea3d5da002c/dqc_reference
[2024-01-25 18:07:06,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:06,860] [INFO] Task started: Prodigal
[2024-01-25 18:07:06,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a6a3fe8-40aa-4de2-b9c7-23b95aeec670/GCF_009834875.1_ASM983487v1_genomic.fna.gz | prodigal -d GCF_009834875.1_ASM983487v1_genomic.fna/cds.fna -a GCF_009834875.1_ASM983487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:22,879] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:22,879] [INFO] Task started: HMMsearch
[2024-01-25 18:07:22,879] [INFO] Running command: hmmsearch --tblout GCF_009834875.1_ASM983487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb2222983-f2b3-46d9-9851-fea3d5da002c/dqc_reference/reference_markers.hmm GCF_009834875.1_ASM983487v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:23,163] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:23,164] [INFO] Found 6/6 markers.
[2024-01-25 18:07:23,210] [INFO] Query marker FASTA was written to GCF_009834875.1_ASM983487v1_genomic.fna/markers.fasta
[2024-01-25 18:07:23,210] [INFO] Task started: Blastn
[2024-01-25 18:07:23,210] [INFO] Running command: blastn -query GCF_009834875.1_ASM983487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2222983-f2b3-46d9-9851-fea3d5da002c/dqc_reference/reference_markers.fasta -out GCF_009834875.1_ASM983487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:23,785] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:23,788] [INFO] Selected 30 target genomes.
[2024-01-25 18:07:23,789] [INFO] Target genome list was writen to GCF_009834875.1_ASM983487v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:23,808] [INFO] Task started: fastANI
[2024-01-25 18:07:23,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a6a3fe8-40aa-4de2-b9c7-23b95aeec670/GCF_009834875.1_ASM983487v1_genomic.fna.gz --refList GCF_009834875.1_ASM983487v1_genomic.fna/target_genomes.txt --output GCF_009834875.1_ASM983487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:47,080] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:47,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb2222983-f2b3-46d9-9851-fea3d5da002c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:47,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb2222983-f2b3-46d9-9851-fea3d5da002c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:47,094] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:07:47,094] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:07:47,094] [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
Arcticibacter tournemirensis	strain=DSM 23085	GCA_006716645.1	699437	699437	type	True	78.1417	76	1576	95	below_threshold
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	77.8132	70	1576	95	below_threshold
Arcticibacter tournemirensis	strain=TF5-37.2-LB10	GCA_008690275.1	699437	699437	type	True	77.7747	75	1576	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.6483	55	1576	95	below_threshold
Arcticibacter eurypsychrophilus	strain=MJ9-5	GCA_001730525.1	1434752	1434752	type	True	77.5087	58	1576	95	below_threshold
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	77.486	83	1576	95	below_threshold
Daejeonella oryzae	strain=DSM 19973	GCA_000422945.1	1122943	1122943	type	True	77.2557	89	1576	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.2041	60	1576	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.1371	75	1576	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	77.067	65	1576	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.0451	69	1576	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	77.0362	59	1576	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	76.9259	90	1576	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	76.8431	58	1576	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	76.8271	92	1576	95	below_threshold
Pedobacter arcticus	strain=A12	GCA_000302595.1	752140	752140	type	True	76.813	53	1576	95	below_threshold
Pararcticibacter amylolyticus	strain=FJ4-8	GCA_003130405.1	2173175	2173175	type	True	76.7884	86	1576	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	76.781	71	1576	95	below_threshold
Mucilaginibacter ginsenosidivorans	strain=Gsoil 3017	GCA_007971025.1	398053	398053	type	True	76.7434	67	1576	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	76.7266	74	1576	95	below_threshold
Mucilaginibacter yixingensis	strain=DSM 26809	GCA_003050755.1	1295612	1295612	type	True	76.7122	67	1576	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	76.3603	96	1576	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.3397	66	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:47,095] [INFO] DFAST Taxonomy check result was written to GCF_009834875.1_ASM983487v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:47,096] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:47,096] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:47,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb2222983-f2b3-46d9-9851-fea3d5da002c/dqc_reference/checkm_data
[2024-01-25 18:07:47,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:47,142] [INFO] Task started: CheckM
[2024-01-25 18:07:47,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009834875.1_ASM983487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009834875.1_ASM983487v1_genomic.fna/checkm_input GCF_009834875.1_ASM983487v1_genomic.fna/checkm_result
[2024-01-25 18:08:33,570] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:33,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:33,603] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:33,603] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:33,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009834875.1_ASM983487v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:33,605] [INFO] Task started: Blastn
[2024-01-25 18:08:33,605] [INFO] Running command: blastn -query GCF_009834875.1_ASM983487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb2222983-f2b3-46d9-9851-fea3d5da002c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009834875.1_ASM983487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:34,421] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:34,426] [INFO] Selected 28 target genomes.
[2024-01-25 18:08:34,426] [INFO] Target genome list was writen to GCF_009834875.1_ASM983487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:34,451] [INFO] Task started: fastANI
[2024-01-25 18:08:34,451] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a6a3fe8-40aa-4de2-b9c7-23b95aeec670/GCF_009834875.1_ASM983487v1_genomic.fna.gz --refList GCF_009834875.1_ASM983487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009834875.1_ASM983487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:58,790] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:58,805] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:08:58,805] [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_009834875.1	s__HMF7647 sp009834875	100.0	1573	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__HMF7647	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017355835.1	s__SYSU-D00535 sp017355835	77.9525	61	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008274585.1	s__BS3 sp008274585	77.7703	106	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__BS3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007846085.1	s__Mucilaginibacter sp007846085	77.5923	56	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001730525.1	s__Arcticibacter eurypsychrophilus	77.4571	59	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001596135.1	s__Mucilaginibacter sp001596135	77.4225	68	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017355785.1	s__SYSU-D00535 sp017355785	77.4008	67	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__SYSU-D00535	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422945.1	s__Daejeonella oryzae	77.2557	89	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834915.1	s__HMF7056 sp009834915	77.1628	81	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__HMF7056	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576455.2	s__Mucilaginibacter celer	77.1371	75	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380615.1	s__JACMJM01 sp014380615	77.0974	81	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__JACMJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116445.1	s__Pedobacter sp005116445	77.0362	59	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797815.1	s__Mucilaginibacter auburnensis	76.9388	64	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002257025.1	s__Daejeonella sp002257025	76.8327	69	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900142915.1	s__Mucilaginibacter sp900142915	76.8147	78	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000302595.1	s__Pelobium arcticum	76.813	53	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101875.1	s__Mucilaginibacter pineti	76.8067	93	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	76.7266	74	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003050755.1	s__Mucilaginibacter yixingensis	76.7122	67	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288635.1	s__Mucilaginibacter sp002288635	76.5501	69	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	76.3811	95	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432115.1	s__Mucilaginibacter sp003432115	76.3397	66	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887275.1	s__Mucilaginibacter sp903887275	75.8735	58	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913935.1	s__Mucilaginibacter sp903913935	75.7895	58	1576	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:58,807] [INFO] GTDB search result was written to GCF_009834875.1_ASM983487v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:58,807] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:58,811] [INFO] DFAST_QC result json was written to GCF_009834875.1_ASM983487v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:58,811] [INFO] DFAST_QC completed!
[2024-01-25 18:08:58,812] [INFO] Total running time: 0h1m53s