[2024-01-24 12:39:41,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:41,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:41,709] [INFO] DQC Reference Directory: /var/lib/cwl/stga8641a14-6499-499e-8b94-655b6011f704/dqc_reference
[2024-01-24 12:39:43,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:43,158] [INFO] Task started: Prodigal
[2024-01-24 12:39:43,159] [INFO] Running command: gunzip -c /var/lib/cwl/stg4640d46c-4b4f-436c-bdf0-a12f0ef8616e/GCF_018918285.1_ASM1891828v1_genomic.fna.gz | prodigal -d GCF_018918285.1_ASM1891828v1_genomic.fna/cds.fna -a GCF_018918285.1_ASM1891828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:49,828] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:49,828] [INFO] Task started: HMMsearch
[2024-01-24 12:39:49,828] [INFO] Running command: hmmsearch --tblout GCF_018918285.1_ASM1891828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8641a14-6499-499e-8b94-655b6011f704/dqc_reference/reference_markers.hmm GCF_018918285.1_ASM1891828v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:50,151] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:50,152] [INFO] Found 6/6 markers.
[2024-01-24 12:39:50,192] [INFO] Query marker FASTA was written to GCF_018918285.1_ASM1891828v1_genomic.fna/markers.fasta
[2024-01-24 12:39:50,193] [INFO] Task started: Blastn
[2024-01-24 12:39:50,193] [INFO] Running command: blastn -query GCF_018918285.1_ASM1891828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8641a14-6499-499e-8b94-655b6011f704/dqc_reference/reference_markers.fasta -out GCF_018918285.1_ASM1891828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:50,861] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:50,865] [INFO] Selected 24 target genomes.
[2024-01-24 12:39:50,865] [INFO] Target genome list was writen to GCF_018918285.1_ASM1891828v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:50,874] [INFO] Task started: fastANI
[2024-01-24 12:39:50,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg4640d46c-4b4f-436c-bdf0-a12f0ef8616e/GCF_018918285.1_ASM1891828v1_genomic.fna.gz --refList GCF_018918285.1_ASM1891828v1_genomic.fna/target_genomes.txt --output GCF_018918285.1_ASM1891828v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:06,857] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:06,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8641a14-6499-499e-8b94-655b6011f704/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:06,858] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8641a14-6499-499e-8b94-655b6011f704/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:06,874] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:06,874] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:06,875] [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
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	100.0	1331	1331	95	conclusive
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	79.0153	432	1331	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	78.7447	415	1331	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_011017965.1	1491	1491	type	True	78.5694	261	1331	95	below_threshold
Clostridium botulinum	strain=ATCC 25763	GCA_001276985.1	1491	1491	type	True	78.5635	263	1331	95	below_threshold
Clostridium combesii	strain=DSM 20696	GCA_002749945.1	39481	39481	type	True	78.5039	249	1331	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	78.2727	277	1331	95	below_threshold
Clostridium aciditolerans	strain=DSM 17425	GCA_016316925.1	339861	339861	type	True	77.9217	197	1331	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	77.737	286	1331	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	77.3794	215	1331	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	77.1637	226	1331	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	76.9625	189	1331	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	76.927	123	1331	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	76.8175	244	1331	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	76.8173	125	1331	95	below_threshold
Clostridium acetobutylicum	strain=ATCC 824	GCA_000008765.1	1488	1488	type	True	76.4423	108	1331	95	below_threshold
Clostridium bornimense	strain=type strain: M2/40	GCA_000577895.1	1216932	1216932	type	True	76.3885	101	1331	95	below_threshold
Clostridium chromiireducens	strain=DSM 23318	GCA_002029255.1	225345	225345	type	True	76.0967	103	1331	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	76.086	128	1331	95	below_threshold
Tissierella praeacuta	strain=DSM 18095	GCA_900128955.1	43131	43131	type	True	75.5511	66	1331	95	below_threshold
Tissierella praeacuta	strain=NCTC11158	GCA_900460335.1	43131	43131	type	True	75.499	67	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:06,876] [INFO] DFAST Taxonomy check result was written to GCF_018918285.1_ASM1891828v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:06,877] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:06,877] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:06,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8641a14-6499-499e-8b94-655b6011f704/dqc_reference/checkm_data
[2024-01-24 12:40:06,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:06,918] [INFO] Task started: CheckM
[2024-01-24 12:40:06,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018918285.1_ASM1891828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018918285.1_ASM1891828v1_genomic.fna/checkm_input GCF_018918285.1_ASM1891828v1_genomic.fna/checkm_result
[2024-01-24 12:40:34,383] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:34,384] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:34,407] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:34,407] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:34,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018918285.1_ASM1891828v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:34,408] [INFO] Task started: Blastn
[2024-01-24 12:40:34,408] [INFO] Running command: blastn -query GCF_018918285.1_ASM1891828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga8641a14-6499-499e-8b94-655b6011f704/dqc_reference/reference_markers_gtdb.fasta -out GCF_018918285.1_ASM1891828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:35,169] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:35,173] [INFO] Selected 25 target genomes.
[2024-01-24 12:40:35,173] [INFO] Target genome list was writen to GCF_018918285.1_ASM1891828v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:35,191] [INFO] Task started: fastANI
[2024-01-24 12:40:35,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg4640d46c-4b4f-436c-bdf0-a12f0ef8616e/GCF_018918285.1_ASM1891828v1_genomic.fna.gz --refList GCF_018918285.1_ASM1891828v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018918285.1_ASM1891828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:52,307] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:52,332] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:52,332] [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_018918285.1	s__MSJ-11 sp018918285	100.0	1331	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__MSJ-11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000619945.1	s__Clostridium_AO lundense	79.0194	430	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873215.1	s__Clostridium_AO tetanomorphum	78.7153	418	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	99.85	99.71	0.98	0.97	5	-
GCF_001276985.1	s__Clostridium_F botulinum	78.5627	263	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_002995785.1	s__Clostridium_AO liquoris	78.3082	275	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001889325.1	s__Clostridium_F botulinum_A	78.1451	276	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_900626095.1	s__Clostridium_AS rectalis	77.7379	288	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AS	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185645.1	s__Clostridium_AK sp900185645	77.6728	248	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	96.24	95.22	0.84	0.82	3	-
GCF_016908015.1	s__Clostridium_AK pascui	77.6341	248	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012926525.1	s__Clostridium_AM sp012926525	77.3657	216	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038625.1	s__Clostridium_AM carboxidivorans	77.1415	228	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_002008345.1	s__Clostridium_F tepidum	77.0367	216	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_000968375.1	s__Clostridium_AM scatologenes	77.0063	244	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_003606265.1	s__Clostridium septicum	76.9082	124	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCF_002327185.1	s__Clostridium chauvoei	76.8092	120	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_000633595.2	s__Clostridium_AM drakei	76.7252	248	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
GCF_000008765.1	s__Clostridium_S acetobutylicum	76.4611	107	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	99.88	98.04	0.99	0.94	19	-
GCF_000230835.1	s__Clostridium sp000230835	76.3891	122	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.12	96.12	0.82	0.82	2	-
GCF_000300195.1	s__Clostridium_J tunisiense	76.23	128	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	96.47	95.03	0.88	0.88	3	-
GCF_002029255.1	s__Clostridium chromiireducens	76.11	102	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.07	97.40	0.90	0.87	3	-
GCF_001270375.1	s__Clostridium_S sp001270375	76.1081	111	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000424205.1	s__Clostridium_X cadaveris	76.08	105	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	99.52	99.40	0.92	0.82	7	-
GCA_018372555.1	s__Clostridium sp018372555	75.6541	116	1331	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:52,334] [INFO] GTDB search result was written to GCF_018918285.1_ASM1891828v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:52,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:52,340] [INFO] DFAST_QC result json was written to GCF_018918285.1_ASM1891828v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:52,340] [INFO] DFAST_QC completed!
[2024-01-24 12:40:52,340] [INFO] Total running time: 0h1m11s